libSBML Python API
5.10.0
|
{core}
Representation of errors, warnings and other diagnosticsThis class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
When a libSBML operation on SBML content results in an error, or when there is something wrong with the SBML content, the problems are reported as SBMLError objects. These are generally stored in an SBMLErrorLog object; this log object, in turn, is kept in the SBMLDocument object containing the SBML content. Applications can obtain the list of logged errors using SBMLDocument.getErrorLog() and then use the methods provided by SBMLErrorLog to access individual SBMLError objects. (Note that despite the word 'error' in the name, SBMLError objects are used to represent not only 'true' errors, but also warnings and some informational diagnostics. The name is a historical hold-over from early versions of libSBML, in which the object really was only used to report errors.)
Each SBMLError object instance has an identification number that identifies the nature of the problem. This 'error id' number will be up to five digits long, and it will come from one of two sets of static integer constants defined in the interface class libsbml: either the SBML error identifiers (described below) or the XML error identifiers (described in the documentation for the class XMLError). The former set of constants includes all the SBML validation rule numbers listed in the appendices of the SBML specification documents, as well as some additional libSBML-specific error codes.
Error codes are useful mainly for software. For human readers, SBMLError also includes text messages that describe the nature of a given problem. The messages can be accessed using SBMLError.getShortMessage() and SBMLError.getMessage(). The former provides a brief one-line description of the issue, while SBMLError.getMessage() provides a more detailed text, including (if appropriate) references to sections of the SBML specifications where relevant topics are discussed. These text strings are suitable for displaying to human users.
An SBMLError object also contains a category code; its value may be retrieved using the method SBMLError.getCategory(). Category values are drawn from a set of static integer constants defined in libsbml and having names beginning with the characters LIBSBML_CAT_
. The list of possible codes is described in a separate section below. Categories are used to partition errors into distinct conceptual groups. This is principally used by the libSBML validation system to group classes of validation checks. For example, LIBSBML_CAT_IDENTIFIER_CONSISTENCY is the category for tests that check identifier consistency; LIBSBML_CAT_MATHML_CONSISTENCY is the category for MathML consistency checking; and so on.
In addition, SBMLError also has a severity code. Its value may be retrieved using the method SBMLError.getSeverity(). The possible severity values are the same as those reported byXMLError. Severity levels currently range from informational (LIBSBML_SEV_INFO) to fatal errors (LIBSBML_SEV_FATAL). They can be used by an application to evaluate how serious a given problem is.
Finally, SBMLError records the line and column near where the problem occurred in the SBML content. The values may be retrieved using the methods SBMLError.getLine() and SBMLError.getColumn(). We say 'near', because a lot of factors affect how accurate the line/column information ultimately is. For example, different XML parsers have different conventions for which line and column number they report for a particular problem (which makes a difference when a problem involves an opening XML tag on one line and a closing tag on another line). In some situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the SBMLError object to the the value of the maximum unsigned long integer representable on the platform where libSBML is running. (This is equal to the constant named ULONG_MAX
in C and C++.) The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.
The error and warning codes returned by libSBML are listed in the table below. The method SBMLError.getErrorId() returns the error code of a given SBMLError object instance. In the libSBML Python language interface, these error identifiers are currently implemented as static integer constants defined in the interface class libsbml.
In this table, the right-hand columns titled 'L1V1', 'L1V2', etc. refer to Levels and Versions of the SBML specifications, and the entries in each column refer to whether the severity of the condition in that particular Level+Version of SBML. The codes stand for the following:
N | = Not applicable |
I | = Informational |
W | = Warning |
E | = Error |
F | = Fatal |
The text shown in the 'Meaning' is the text returned by the SBMLError.getShortMessage() method on a given SBMLError object. A longer and (hopefully) clearer explanation of the issue is returned by SBMLError.getMessage().
The error codes come from different lists depending on whether they're from libSBML core or from an SBML Level 3 package extension. However, in the language interfaces other than C++, all libSBML error codes are ultimately represented as integer constants rather than separate enumerations lists, and they are all stored in a single interface class. Codes from different libSBML extensions have names that begin with the package's nickname, such as Qual
for the Qualitative Models package, Layout
for the Layout package, and so on. If the name of a code does not begin with one of the package nicknames (Layout
, Fbc
, Comp
, Qual
, etc.), then it is a code from libSBML core.
Enumerator | Meaning | L 1 V 1 | L 1 V 2 | L 2 V 1 | L 2 V 2 | L 2 V 3 | L 2 V 4 | L 3 V 1 |
---|---|---|---|---|---|---|---|---|
UnknownError | Encountered unknown internal libSBML error | F | F | F | F | F | F | F |
NotUTF8 | File does not use UTF-8 encoding | E | E | E | E | E | E | E |
UnrecognizedElement | Encountered unrecognized element | E | E | E | E | E | E | E |
NotSchemaConformant | Document does not conform to the SBML XML schema | E | E | E | E | E | E | E |
L3NotSchemaConformant | Document is not well-formed XML | N | N | N | N | N | N | E |
InvalidMathElement | Invalid MathML | N | N | E | E | E | E | E |
DisallowedMathMLSymbol | Disallowed MathML symbol found | N | N | E | E | E | E | E |
DisallowedMathMLEncodingUse | Use of the MathML 'encoding' attribute is not allowed on this element | N | N | E | E | E | E | E |
DisallowedDefinitionURLUse | Use of the MathML 'definitionURL' attribute is not allowed on this element | N | N | E | E | E | E | E |
BadCsymbolDefinitionURLValue | Invalid <csymbol> 'definitionURL' attribute value | N | N | E | E | E | E | E |
DisallowedMathTypeAttributeUse | Use of the MathML 'type' attribute is not allowed on this element | N | N | E | E | E | E | E |
DisallowedMathTypeAttributeValue | Disallowed MathML 'type' attribute value | N | N | E | E | E | E | E |
LambdaOnlyAllowedInFunctionDef | Use of <lambda> not permitted outside of FunctionDefinition objects | N | N | E | E | E | E | E |
BooleanOpsNeedBooleanArgs | Non-Boolean argument given to Boolean operator | N | N | W | E | E | E | E |
NumericOpsNeedNumericArgs | Non-numerical argument given to numerical operator | N | N | W | E | E | E | E |
ArgsToEqNeedSameType | Arguments to <eq> and <neq> must have the same data types | N | N | W | E | E | E | E |
PiecewiseNeedsConsistentTypes | Terms in a <piecewise> expression must have consistent data types | N | N | W | E | E | E | E |
PieceNeedsBoolean | The second argument of a <piece> expression must yield a Boolean value | N | N | W | E | E | E | E |
ApplyCiMustBeUserFunction | A <ci> element in this context must refer to a function definition | N | N | W | E | E | E | E |
ApplyCiMustBeModelComponent | A <ci> element in this context must refer to a model component | N | N | W | E | E | E | E |
KineticLawParametersAreLocalOnly | Cannot use a KineticLaw local parameter outside of its local scope | N | N | W | E | E | E | E |
MathResultMustBeNumeric | A formula's result in this context must be a numerical value | N | N | W | E | E | E | E |
OpsNeedCorrectNumberOfArgs | Incorrect number of arguments given to MathML operator | N | N | W | E | E | E | E |
InvalidNoArgsPassedToFunctionDef | Incorrect number of arguments given to function invocation | N | N | N | N | N | E | E |
DisallowedMathUnitsUse | Attribute 'units' is only permitted on <cn> elements | N | N | N | N | N | N | E |
InvalidUnitsValue | Invalid value given for the 'units' attribute | N | N | N | N | N | N | E |
DuplicateComponentId | Duplicate 'id' attribute value | E | E | E | E | E | E | E |
DuplicateUnitDefinitionId | Duplicate unit definition 'id' attribute value | E | E | E | E | E | E | E |
DuplicateLocalParameterId | Duplicate local parameter 'id' attribute value | E | E | E | E | E | E | E |
MultipleAssignmentOrRateRules | Multiple rules for the same variable are not allowed | E | E | E | E | E | E | E |
MultipleEventAssignmentsForId | Multiple event assignments for the same variable are not allowed | N | N | E | E | E | E | E |
EventAndAssignmentRuleForId | An event assignment and an assignment rule must not have the same value for 'variable' | N | N | E | E | E | E | E |
DuplicateMetaId | Duplicate 'metaid' attribute value | N | N | E | E | E | E | E |
InvalidSBOTermSyntax | Invalid syntax for an 'sboTerm' attribute value | N | N | N | E | E | E | E |
InvalidMetaidSyntax | Invalid syntax for a 'metaid' attribute value | N | N | E | E | E | E | E |
InvalidIdSyntax | Invalid syntax for an 'id' attribute value | E | E | E | E | E | E | E |
InvalidUnitIdSyntax | Invalid syntax for the identifier of a unit | N | N | N | E | E | E | E |
InvalidNameSyntax | Invalid syntax for a 'name' attribute value | N | N | N | N | N | N | E |
MissingAnnotationNamespace | Missing declaration of the XML namespace for the annotation | N | N | N | E | E | E | E |
DuplicateAnnotationNamespaces | Multiple annotations using the same XML namespace | N | N | N | E | E | E | E |
SBMLNamespaceInAnnotation | The SBML XML namespace cannot be used in an Annotation object | N | N | N | E | E | E | N |
MultipleAnnotations | Only one Annotation object is permitted under a given SBML object | N | N | N | N | N | N | E |
InconsistentArgUnits | The units of the function call's arguments are not consistent with its definition | W | W | W | E | E | W | W |
InconsistentKineticLawUnitsL3 | The kinetic law's units are inconsistent with those of other kinetic laws in the model | N | N | N | N | N | N | W |
AssignRuleCompartmentMismatch | Mismatched units in assignment rule for compartment | E | E | E | E | E | W | W |
AssignRuleSpeciesMismatch | Mismatched units in assignment rule for species | E | E | E | E | E | W | W |
AssignRuleParameterMismatch | Mismatched units in assignment rule for parameter | E | E | E | E | E | W | W |
AssignRuleStoichiometryMismatch | Mismatched units in assignment rule for stoichiometry | N | N | N | N | N | N | W |
InitAssignCompartmenMismatch | Mismatched units in initial assignment to compartment | N | N | N | E | E | W | W |
InitAssignSpeciesMismatch | Mismatched units in initial assignment to species | N | N | N | E | E | W | W |
InitAssignParameterMismatch | Mismatched units in initial assignment to parameter | N | N | N | E | E | W | W |
InitAssignStoichiometryMismatch | Mismatched units in initial assignment to stoichiometry | N | N | N | N | N | N | W |
RateRuleCompartmentMismatch | Mismatched units in rate rule for compartment | E | E | E | E | E | W | W |
RateRuleSpeciesMismatch | Mismatched units in rate rule for species | E | E | E | E | E | W | W |
RateRuleParameterMismatch | Mismatched units in rate rule for parameter | E | E | E | E | E | W | W |
RateRuleStoichiometryMismatch | Mismatched units in rate rule for stoichiometry | N | N | N | N | N | N | W |
KineticLawNotSubstancePerTime | The units of the kinetic law are not 'substance'/'time' | E | E | E | E | E | W | W |
SpeciesInvalidExtentUnits | The species' units are not consistent with units of extent | N | N | N | N | N | N | W |
DelayUnitsNotTime | The units of the delay expression are not units of time | N | N | E | E | E | W | W |
EventAssignCompartmentMismatch | Mismatched units in event assignment for compartment | N | N | E | E | E | W | W |
EventAssignSpeciesMismatch | Mismatched units in event assignment for species | N | N | E | E | E | W | W |
EventAssignParameterMismatch | Mismatched units in event assignment for parameter | N | N | E | E | E | W | W |
EventAssignStoichiometryMismatch | Mismatched units in event assignment for stoichiometry | N | N | N | N | N | N | W |
PriorityUnitsNotDimensionless | The units of a priority expression must be 'dimensionless' | N | N | N | N | N | N | W |
UpperUnitBound | Upper boundary of unit validation diagnostic codes | N | N | N | N | N | N | N |
OverdeterminedSystem | The model is overdetermined | W | W | W | E | E | E | E |
InvalidModelSBOTerm | Invalid 'sboTerm' attribute value for a Model object | N | N | N | E | E | W | W |
InvalidFunctionDefSBOTerm | Invalid 'sboTerm' attribute value for a FunctionDefinition object | N | N | N | E | E | W | W |
InvalidParameterSBOTerm | Invalid 'sboTerm' attribute value for a Parameter object | N | N | N | E | E | W | W |
InvalidInitAssignSBOTerm | Invalid 'sboTerm' attribute value for an InitialAssignment object | N | N | N | E | E | W | W |
InvalidRuleSBOTerm | Invalid 'sboTerm' attribute value for a Rule object | N | N | N | E | E | W | W |
InvalidConstraintSBOTerm | Invalid 'sboTerm' attribute value for a Constraint object | N | N | N | E | E | W | W |
InvalidReactionSBOTerm | Invalid 'sboTerm' attribute value for a Reaction object | N | N | N | E | E | W | W |
InvalidSpeciesReferenceSBOTerm | Invalid 'sboTerm' attribute value for a SpeciesReference object | N | N | N | E | E | W | W |
InvalidKineticLawSBOTerm | Invalid 'sboTerm' attribute value for a KineticLaw object | N | N | N | E | E | W | W |
InvalidEventSBOTerm | Invalid 'sboTerm' attribute value for an Event object | N | N | N | E | E | W | W |
InvalidEventAssignmentSBOTerm | Invalid 'sboTerm' attribute value for an EventAssignment object | N | N | N | E | E | W | W |
InvalidCompartmentSBOTerm | Invalid 'sboTerm' attribute value for a Compartment object | N | N | N | N | E | W | W |
InvalidSpeciesSBOTerm | Invalid 'sboTerm' attribute value for a Species object | N | N | N | N | E | W | W |
InvalidCompartmentTypeSBOTerm | Invalid 'sboTerm' attribute value for a CompartmentType object | N | N | N | N | E | W | N |
InvalidSpeciesTypeSBOTerm | Invalid 'sboTerm' attribute value for a SpeciesType object | N | N | N | N | E | W | N |
InvalidTriggerSBOTerm | Invalid 'sboTerm' attribute value for an Event Trigger object | N | N | N | N | E | W | W |
InvalidDelaySBOTerm | Invalid 'sboTerm' attribute value for an Event Delay object | N | N | N | N | E | W | W |
NotesNotInXHTMLNamespace | Notes must be placed in the XHTML XML namespace | E | E | E | E | E | E | E |
NotesContainsXMLDecl | XML declarations are not permitted in Notes objects | N | N | N | E | E | E | E |
NotesContainsDOCTYPE | XML DOCTYPE elements are not permitted in Notes objects | N | N | N | E | E | E | E |
InvalidNotesContent | Invalid notes content found | N | N | N | E | E | E | N |
OnlyOneNotesElementAllowed | Only one Notes subobject is permitted on a given SBML object | N | N | N | N | N | N | E |
InvalidNamespaceOnSBML | Invalid XML namespace for the SBML container element | E | E | E | E | E | E | E |
MissingOrInconsistentLevel | Missing or inconsistent value for the 'level' attribute | E | E | E | E | E | E | E |
MissingOrInconsistentVersion | Missing or inconsistent value for the 'version' attribute | E | E | E | E | E | E | E |
PackageNSMustMatch | Inconsistent or invalid SBML Level/Version for the package namespace declaration | N | N | N | N | N | N | E |
LevelPositiveInteger | The 'level' attribute must have a positive integer value | N | N | N | N | N | N | E |
VersionPositiveInteger | The 'version' attribute must have a positive integer value | N | N | N | N | N | N | E |
AllowedAttributesOnSBML | Invalid attribute found on the SBML container element | N | N | N | N | N | N | E |
L3PackageOnLowerSBML | An L3 package ns found on the SBML container element. | W | W | W | W | W | W | N |
MissingModel | No model definition found | E | E | E | E | E | E | E |
IncorrectOrderInModel | Incorrect ordering of components within the Model object | E | E | E | E | E | E | N |
EmptyListElement | Empty ListOf___ object found | E | E | E | E | E | E | E |
NeedCompartmentIfHaveSpecies | The presence of a species requires a compartment | E | E | E | E | E | E | E |
OneOfEachListOf | Only one of each kind of ListOf___ object is allowed inside a Model object | N | N | N | N | N | N | E |
OnlyFuncDefsInListOfFuncDefs | Only FunctionDefinition, Notes and Annotation objects are allowed in ListOfFunctionDefinitions | N | N | N | N | N | N | E |
OnlyUnitDefsInListOfUnitDefs | Only UnitDefinition, Notes and Annotation objects are allowed in ListOfUnitDefinitions objects | N | N | N | N | N | N | E |
OnlyCompartmentsInListOfCompartments | Only Compartment, Notes and Annotation objects are allowed in ListOfCompartments objects | N | N | N | N | N | N | E |
OnlySpeciesInListOfSpecies | Only Species, Notes and Annotation objects are allowed in ListOfSpecies objects | N | N | N | N | N | N | E |
OnlyParametersInListOfParameters | Only Parameter, Notes and Annotation objects are allowed in ListOfParameters objects | N | N | N | N | N | N | E |
OnlyInitAssignsInListOfInitAssigns | Only InitialAssignment, Notes and Annotation objects are allowed in ListOfInitialAssignments objects | N | N | N | N | N | N | E |
OnlyRulesInListOfRules | Only Rule, Notes and Annotation objects are allowed in ListOfRules objects | N | N | N | N | N | N | E |
OnlyConstraintsInListOfConstraints | Only Constraint, Notes and Annotation objects are allowed in ListOfConstraints objects | N | N | N | N | N | N | E |
OnlyReactionsInListOfReactions | Only Reaction, Notes and Annotation objects are allowed in ListOfReactions objects | N | N | N | N | N | N | E |
OnlyEventsInListOfEvents | Only Event, Notes and Annotation objects are allowed in ListOfEvents objects | N | N | N | N | N | N | E |
L3ConversionFactorOnModel | A 'conversionFactor' attribute value must reference a Parameter object | N | N | N | N | N | N | E |
L3TimeUnitsOnModel | Invalid 'timeUnits' attribute value | N | N | N | N | N | N | W |
L3VolumeUnitsOnModel | Invalid 'volumeUnits' attribute value | N | N | N | N | N | N | W |
L3AreaUnitsOnModel | Invalid 'areaUnits' attribute value | N | N | N | N | N | N | W |
L3LengthUnitsOnModel | Invalid 'lengthUnits' attribute value | N | N | N | N | N | N | W |
L3ExtentUnitsOnModel | Invalid 'extentUnits' attribute value | N | N | N | N | N | N | W |
AllowedAttributesOnModel | Invalid attribute found on the Model object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfFuncs | Invalid attribute found on the ListOfFunctionDefinitions object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfUnitDefs | Invalid attribute found on the ListOfUnitDefinitions object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfComps | Invalid attribute found on the ListOfCompartments object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfSpecies | Invalid attribute found on the ListOfSpecies object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfParams | Invalid attribute found on the ListOfParameters object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfInitAssign | Invalid attribute found on the ListOfInitialAssignments object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfRules | Invalid attribute found on the ListOfRules object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfConstraints | Invalid attribute found on the ListOfConstraints object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfReactions | Invalid attribute found on the ListOfReactions object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfEvents | Invalid attribute found on the ListOfEvents object | N | N | N | N | N | N | E |
FunctionDefMathNotLambda | Invalid expression found in the function definition | N | N | E | E | E | E | E |
InvalidApplyCiInLambda | Invalid forward reference in the MathML <apply> <ci> ...</ci> </apply> expression | N | N | E | E | E | N | N |
RecursiveFunctionDefinition | Recursive function definitions are not permitted | N | N | E | E | E | E | E |
InvalidCiInLambda | Invalid <ci> reference found inside the <lambda> mathematical formula | N | N | E | E | E | E | E |
InvalidFunctionDefReturnType | A function's return type must be either a number or a Boolean | N | N | E | E | E | E | E |
OneMathElementPerFunc | A FunctionDefinition object must contain one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnFunc | Invalid attribute found on the FunctionDefinition object | N | N | N | N | N | N | E |
InvalidUnitDefId | Invalid 'id' attribute value for a UnitDefinition object | E | E | E | E | E | E | E |
InvalidSubstanceRedefinition | Invalid redefinition of built-in type 'substance' | E | E | E | E | E | E | N |
InvalidLengthRedefinition | Invalid redefinition of built-in type 'length' | W | W | E | E | E | E | N |
InvalidAreaRedefinition | Invalid redefinition of built-in type name 'area' | W | W | E | E | E | E | N |
InvalidTimeRedefinition | Invalid redefinition of built-in type name 'time' | E | E | E | E | E | E | N |
InvalidVolumeRedefinition | Invalid redefinition of built-in type name 'volume' | E | E | E | E | E | E | N |
VolumeLitreDefExponentNotOne | Must use 'exponent'=1 when defining 'volume' in terms of litres | E | E | E | E | E | N | N |
VolumeMetreDefExponentNot3 | Must use 'exponent'=3 when defining 'volume' in terms of metres | N | N | E | E | E | N | N |
EmptyListOfUnits | An empty list of Unit objects is not permitted in a UnitDefinition object | E | E | E | E | E | E | N |
InvalidUnitKind | Invalid value for the 'kind' attribute of a UnitDefinition object | E | E | E | E | E | E | E |
OffsetNoLongerValid | Unit attribute 'offset' is not supported in this Level+Version of SBML | N | N | N | E | E | E | N |
CelsiusNoLongerValid | Unit name 'Celsius' is not defined in this Level+Version of SBML | N | N | N | E | E | E | N |
EmptyUnitListElement | A ListOfUnits object must not be empty | N | N | N | N | N | N | E |
OneListOfUnitsPerUnitDef | At most one ListOfUnits object is allowed inside a UnitDefinition object | N | N | N | N | N | N | E |
OnlyUnitsInListOfUnits | Only Unit, Notes and Annotation objects are allowed in ListOfUnits objects | N | N | N | N | N | N | E |
AllowedAttributesOnUnitDefinition | Invalid attribute found on the UnitDefinition object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfUnits | Invalid attribute found on the ListOfUnits object | N | N | N | N | N | N | E |
AllowedAttributesOnUnit | Invalid attribute found on the Unit object | N | N | N | N | N | N | E |
ZeroDimensionalCompartmentSize | Invalid use of the 'size' attribute for a zero-dimensional compartment | N | N | E | E | E | E | N |
ZeroDimensionalCompartmentUnits | Invalid use of the 'units' attribute for a zero-dimensional compartment | N | N | E | E | E | E | N |
ZeroDimensionalCompartmentConst | Zero-dimensional compartments must be defined to be constant | N | N | E | E | E | E | N |
UndefinedOutsideCompartment | Invalid value for the 'outside' attribute of a Compartment object | E | E | E | E | E | E | N |
RecursiveCompartmentContainment | Recursive nesting of compartments via the 'outside' attribute is not permitted | W | W | W | E | E | E | N |
ZeroDCompartmentContainment | Invalid nesting of zero-dimensional compartments | N | N | W | E | E | E | N |
Invalid1DCompartmentUnits | Invalid value for the 'units' attribute of a one-dimensional compartment | N | N | E | E | E | E | W |
Invalid2DCompartmentUnits | Invalid value for the 'units' attribute of a two-dimensional compartment | N | N | E | E | E | E | W |
Invalid3DCompartmentUnits | Invalid value for the 'units' attribute of a three-dimensional compartment | E | E | E | E | E | E | W |
InvalidCompartmentTypeRef | Invalid value for the 'compartmentType' attribute of a compartment | N | N | N | E | E | E | N |
OneDimensionalCompartmentUnits | No units defined for 1-D compartment | N | N | N | N | N | N | W |
TwoDimensionalCompartmentUnits | No units defined for 2-D compartment | N | N | N | N | N | N | W |
ThreeDimensionalCompartmentUnits | No units defined for 3-D Compartment object | N | N | N | N | N | N | W |
AllowedAttributesOnCompartment | Invalid attribute found on Compartment object | N | N | N | N | N | N | E |
NoUnitsOnCompartment | No units defined for Compartment object | N | N | N | N | N | N | W |
InvalidSpeciesCompartmentRef | Invalid value found for Species 'compartment' attribute | E | E | E | E | E | E | E |
HasOnlySubsNoSpatialUnits | Attribute 'spatialSizeUnits' must not be set if 'hasOnlySubstanceUnits'='true' | N | N | E | E | N | N | N |
NoSpatialUnitsInZeroD | Attribute 'spatialSizeUnits' must not be set if the compartment is zero-dimensional | N | N | E | E | N | N | N |
NoConcentrationInZeroD | Attribute 'initialConcentration' must not be set if the compartment is zero-dimensional | N | N | E | E | E | E | N |
SpatialUnitsInOneD | Invalid value for 'spatialSizeUnits' attribute of a one-dimensional compartment | N | N | E | E | N | N | N |
SpatialUnitsInTwoD | Invalid value for the 'spatialSizeUnits' attribute of a two-dimensional compartment | N | N | E | E | N | N | N |
SpatialUnitsInThreeD | Invalid value for the 'spatialSizeUnits' attribute of a three-dimensional compartment | N | N | E | E | N | N | N |
InvalidSpeciesSusbstanceUnits | Invalid value for a Species 'units' attribute | E | E | E | E | E | E | W |
BothAmountAndConcentrationSet | Cannot set both 'initialConcentration' and 'initialAmount' attributes simultaneously | N | N | E | E | E | E | E |
NonBoundarySpeciesAssignedAndUsed | Cannot use a non-boundary species in both reactions and rules simultaneously | W | W | E | E | E | E | E |
NonConstantSpeciesUsed | Cannot use a constant, non-boundary species as a reactant or product | N | N | E | E | E | E | E |
InvalidSpeciesTypeRef | Invalid value for the 'speciesType' attribute of a species | N | N | N | E | E | E | N |
MultSpeciesSameTypeInCompartment | Cannot have multiple species of the same species type in the same compartment | N | N | N | E | E | E | N |
MissingSpeciesCompartment | Missing value for the 'compartment' attribute | E | E | E | E | E | E | E |
SpatialSizeUnitsRemoved | Attribute 'spatialSizeUnits' is not supported in this Level+Version of SBML | N | N | N | N | E | E | N |
SubstanceUnitsOnSpecies | No substance units defined for the species | N | N | N | N | N | N | W |
ConversionFactorOnSpecies | Invalid value for the 'conversionFactor' attribute | N | N | N | N | N | N | E |
AllowedAttributesOnSpecies | Invalid attribute found on Species object | N | N | N | N | N | N | E |
InvalidParameterUnits | Invalid value for the 'units' attribute of a Parameter object | E | E | E | E | E | E | W |
ParameterUnits | No units defined for the parameter | N | N | N | N | N | N | W |
ConversionFactorMustConstant | A conversion factor must reference a Parameter object declared to be a constant | N | N | N | N | N | N | E |
AllowedAttributesOnParameter | Invalid attribute found on Parameter object | N | N | N | N | N | N | E |
InvalidInitAssignSymbol | Invalid value for the 'symbol' attribute of an InitialAssignment object | N | N | N | E | E | E | E |
MultipleInitAssignments | Multiple initial assignments for the same 'symbol' value are not allowed | N | N | N | E | E | E | E |
InitAssignmentAndRuleForSameId | Cannot set a value using both an initial assignment and an assignment rule simultaneously | N | N | N | E | E | E | E |
OneMathElementPerInitialAssign | An InitialAssignment object must contain one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnInitialAssign | Invalid attribute found on an InitialAssignment object | N | N | N | N | N | N | E |
InvalidAssignRuleVariable | Invalid value for the 'variable' attribute of an AssignmentRule object | E | E | E | E | E | E | E |
InvalidRateRuleVariable | Invalid value for the 'variable' attribute of a RateRule object | E | E | E | E | E | E | E |
AssignmentToConstantEntity | An assignment rule cannot assign an entity declared to be constant | N | N | E | E | E | E | E |
RateRuleForConstantEntity | A rate rule cannot assign an entity declared to be constant | N | N | E | E | E | E | E |
CircularRuleDependency | Circular dependencies involving rules and reactions are not permitted | N | N | N | E | E | E | E |
OneMathElementPerRule | A rule object must contain one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnAssignRule | Invalid attribute found on an AssignmentRule object | N | N | N | N | N | N | E |
AllowedAttributesOnRateRule | Invalid attribute found on a RateRule object | N | N | N | N | N | N | E |
AllowedAttributesOnAlgRule | Invalid attribute found on an AlgebraicRule object | N | N | N | N | N | N | E |
ConstraintMathNotBoolean | A Constraint object's <math> must evaluate to a Boolean value | N | N | N | E | E | E | E |
IncorrectOrderInConstraint | Subobjects inside the Constraint object are not in the prescribed order | N | N | N | E | E | E | N |
ConstraintNotInXHTMLNamespace | A Constraint's Message subobject must be in the XHTML XML namespace | N | N | N | E | E | E | N |
ConstraintContainsXMLDecl | XML declarations are not permitted within Constraint's Message objects | N | N | N | E | E | E | E |
ConstraintContainsDOCTYPE | XML DOCTYPE elements are not permitted within Constraint's Message objects | N | N | N | E | E | E | E |
InvalidConstraintContent | Invalid content for a Constraint object's Message object | N | N | N | E | E | E | N |
OneMathElementPerConstraint | A Constraint object must contain one <math> element | N | N | N | N | N | N | E |
OneMessageElementPerConstraint | A Constraint object must contain one Message subobject | N | N | N | N | N | N | E |
AllowedAttributesOnConstraint | Invalid attribute found on Constraint object | N | N | N | N | N | N | E |
NoReactantsOrProducts | Cannot have a reaction with neither reactants nor products | E | E | E | E | E | E | E |
IncorrectOrderInReaction | Subobjects inside the Reaction object are not in the prescribed order | E | E | E | E | E | E | N |
EmptyListInReaction | Reaction components, if present, cannot be empty | E | E | E | E | E | E | E |
InvalidReactantsProductsList | Invalid object found in the list of reactants or products | E | E | E | E | E | E | E |
InvalidModifiersList | Invalid object found in the list of modifiers | N | N | E | E | E | E | E |
OneSubElementPerReaction | A Reaction object can only contain one of each allowed type of object | N | N | N | N | N | N | E |
CompartmentOnReaction | Invalid value for the Reaction 'compartment' attribute | N | N | N | N | N | N | E |
AllowedAttributesOnReaction | Invalid attribute for a Reaction object | N | N | N | N | N | N | E |
InvalidSpeciesReference | Invalid 'species' attribute value in SpeciesReference object | E | E | E | E | E | E | E |
BothStoichiometryAndMath | The 'stoichiometry' attribute and StoichiometryMath subobject are mutually exclusive | N | N | E | E | E | E | N |
AllowedAttributesOnSpeciesReference | Invalid attribute found on the SpeciesReference object | N | N | N | N | N | N | E |
AllowedAttributesOnModifier | Invalid attribute found on the ModifierSpeciesReference object | N | N | N | N | N | N | E |
UndeclaredSpeciesRef | Unknown species referenced in the kinetic law <math> formula | W | W | E | E | E | E | E |
IncorrectOrderInKineticLaw | Incorrect ordering of components in the KineticLaw object | N | N | E | E | E | E | N |
EmptyListInKineticLaw | The list of parameters, if present, cannot be empty | E | E | E | E | E | E | E |
NonConstantLocalParameter | Parameters local to a KineticLaw object must have a 'constant' attribute value of 'true' | N | N | W | E | E | E | N |
SubsUnitsNoLongerValid | Attribute 'substanceUnits' is not supported in this Level+Version of SBML | N | N | N | E | E | E | N |
TimeUnitsNoLongerValid | Attribute 'timeUnits' is not supported in this Level+Version of SBML | N | N | N | E | E | E | N |
OneListOfPerKineticLaw | Only one ListOfLocalParameters object is permitted within a KineticLaw object | N | N | N | N | N | N | E |
OnlyLocalParamsInListOfLocalParams | Only LocalParameter, Notes and Annotation objects are allowed in ListOfLocalParameter objects | N | N | N | N | N | N | E |
AllowedAttributesOnListOfLocalParam | Invalid attribute found on the ListOfLocalParameters object | N | N | N | N | N | N | E |
OneMathPerKineticLaw | Only one <math> element is allowed in a KineticLaw object | N | N | E | E | E | E | E |
UndeclaredSpeciesInStoichMath | Unknown species referenced in the StoichiometryMath object's <math> formula | N | N | W | E | E | E | N |
AllowedAttributesOnKineticLaw | Invalid attribute found on the KineticLaw object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfSpeciesRef | Invalid attribute found on the ListOfSpeciesReferences object | N | N | N | N | N | N | E |
AllowedAttributesOnListOfMods | Invalid attribute found on the ListOfModifiers object | N | N | N | N | N | N | E |
AllowedAttributesOnLocalParameter | Invalid attribute found on the LocalParameter object | N | N | N | N | N | N | E |
MissingTriggerInEvent | The Event object is missing a Trigger subobject | N | N | E | E | E | E | E |
TriggerMathNotBoolean | A Trigger object's <math> expression must evaluate to a Boolean value | N | N | E | E | E | E | E |
MissingEventAssignment | The Event object is missing an EventAssignment subobject | N | N | E | E | E | E | E |
TimeUnitsEvent | Units referenced by 'timeUnits' attribute are not compatible with units of time | N | N | E | E | N | N | N |
IncorrectOrderInEvent | Incorrect ordering of components in Event object | N | N | E | E | E | E | N |
ValuesFromTriggerTimeNeedDelay | Attribute 'useValuesFromTriggerTime'='false', but the Event object does not define a delay | N | N | N | N | N | E | N |
DelayNeedsValuesFromTriggerTime | The use of a Delay object requires the Event attribute 'useValuesFromTriggerTime' | N | N | N | N | N | N | N |
OneMathPerTrigger | A Trigger object must have one <math> element | N | N | N | N | N | N | E |
OneMathPerDelay | A Delay object must have one <math> element | N | N | N | N | N | N | E |
InvalidEventAssignmentVariable | Invalid 'variable' attribute value in Event object | N | N | E | E | E | E | E |
EventAssignmentForConstantEntity | An EventAssignment object cannot assign to a component having attribute 'constant'='true' | N | N | W | E | E | E | E |
OneMathPerEventAssignment | An EventAssignment object must have one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnEventAssignment | Invalid attribute found on the EventAssignment object | N | N | N | N | N | N | E |
OnlyOneDelayPerEvent | An Event object can only have one Delay subobject | N | N | N | N | N | N | E |
OneListOfEventAssignmentsPerEvent | An Event object can only have one ListOfEventAssignments subobject | N | N | N | N | N | N | E |
OnlyEventAssignInListOfEventAssign | Only EventAssignment, Notes and Annotation objects are allowed in ListOfEventAssignments | N | N | N | N | N | N | E |
AllowedAttributesOnListOfEventAssign | Invalid attribute found on the ListOfEventAssignments object | N | N | N | N | N | N | E |
AllowedAttributesOnEvent | Invalid attribute found on the Event object | N | N | N | N | N | N | E |
AllowedAttributesOnTrigger | Invalid attribute found on the Trigger object | N | N | N | N | N | N | E |
AllowedAttributesOnDelay | Invalid attribute found on the Delay object | N | N | N | N | N | N | E |
PersistentNotBoolean | The Trigger attribute 'persistent' must evaluate to a Boolean value | N | N | N | N | N | N | E |
InitialValueNotBoolean | The Trigger attribute 'initialValue' must evaluate to a Boolean value | N | N | N | N | N | N | E |
OnlyOnePriorityPerEvent | An Event object can only have one Priority subobject | N | N | N | N | N | N | E |
OneMathPerPriority | A Priority object must have one <math> element | N | N | N | N | N | N | E |
AllowedAttributesOnPriority | Invalid attribute found on the Priority object | N | N | N | N | N | N | E |
GeneralWarningNotSpecified | Unknown error | N | N | N | N | N | N | N |
CompartmentShouldHaveSize | It's best to define a size for every compartment in a model | N | N | W | W | W | W | W |
SpeciesShouldHaveValue | It's best to define an initial amount or initial concentration for every species in a model | N | N | W | W | W | W | W |
ParameterShouldHaveUnits | It's best to declare units for every parameter in a model | W | W | W | W | W | W | W |
LocalParameterShadowsId | Local parameters defined within a kinetic law shadow global object symbols | W | W | W | W | W | W | W |
CannotConvertToL1V1 | Cannot convert to SBML Level 1 Version 1 | N | E | E | E | E | E | E |
NoEventsInL1 | SBML Level 1 does not support events | N | N | E | E | E | E | E |
NoFunctionDefinitionsInL1 | SBML Level 1 does not support function definitions | N | N | W | W | W | W | W |
NoConstraintsInL1 | SBML Level 1 does not support constraints | N | N | N | W | W | W | W |
NoInitialAssignmentsInL1 | SBML Level 1 does not support initial assignments | N | N | N | W | W | W | W |
NoSpeciesTypesInL1 | SBML Level 1 does not support species types | N | N | N | W | W | W | N |
NoCompartmentTypeInL1 | SBML Level 1 does not support compartment types | N | N | N | W | W | W | N |
NoNon3DCompartmentsInL1 | SBML Level 1 only supports three-dimensional compartments | N | N | E | E | E | E | E |
NoFancyStoichiometryMathInL1 | SBML Level 1 does not support non-integer nor non-rational stoichiometry formulas | N | N | E | E | E | E | E |
NoNonIntegerStoichiometryInL1 | SBML Level 1 does not support non-integer 'stoichiometry' attribute values | N | N | E | E | E | E | E |
NoUnitMultipliersOrOffsetsInL1 | SBML Level 1 does not support multipliers or offsets in unit definitions | N | N | E | E | E | E | E |
SpeciesCompartmentRequiredInL1 | In SBML Level 1, a value for 'compartment' is mandatory in species definitions | N | N | E | E | E | E | E |
NoSpeciesSpatialSizeUnitsInL1 | SBML Level 1 does not support species 'spatialSizeUnits' settings | N | N | E | E | E | E | N |
NoSBOTermsInL1 | SBML Level 1 does not support the 'sboTerm' attribute | N | N | N | W | W | W | W |
StrictUnitsRequiredInL1 | SBML Level 1 requires strict unit consistency | N | N | N | N | N | W | W |
ConversionFactorNotInL1 | SBML Level 1 does not support the 'conversionFactor' attribute | N | N | N | N | N | N | E |
CompartmentNotOnL1Reaction | SBML Level 1 does not support the 'compartment' attribute on Reaction objects | N | N | N | N | N | N | W |
ExtentUnitsNotSubstance | Units of extent must be compatible with units of substance | N | N | N | N | N | N | E |
GlobalUnitsNotDeclared | Global units must be refer to unit kind or unitDefinition. | N | N | N | N | N | N | E |
HasOnlySubstanceUnitsNotinL1 | The concept of hasOnlySubstanceUnits was not available in SBML Level 1. | N | N | E | E | E | E | E |
AvogadroNotSupported | Avogadro not supported in Levels 2 and 1. | N | N | N | N | N | N | E |
NoConstraintsInL2v1 | SBML Level 2 Version 1 does not support Constraint objects | N | N | N | W | W | W | W |
NoInitialAssignmentsInL2v1 | SBML Level 2 Version 1 does not support InitialAssignment objects | N | N | N | W | W | W | W |
NoSpeciesTypeInL2v1 | SBML Level 2 Version 1 does not support SpeciesType objects | N | N | N | W | W | W | N |
NoCompartmentTypeInL2v1 | SBML Level 2 Version 1 does not support CompartmentType objects | N | N | N | W | W | W | N |
NoSBOTermsInL2v1 | SBML Level 2 Version 1 does not support the 'sboTerm' attribute | N | N | N | W | W | W | W |
NoIdOnSpeciesReferenceInL2v1 | SBML Level 2 Version 1 does not support the 'id' attribute on SpeciesReference objects | N | N | N | W | W | W | W |
NoDelayedEventAssignmentInL2v1 | SBML Level 2 Version 1 does not support the 'useValuesFromTriggerTime' attribute | N | N | N | N | N | E | E |
StrictUnitsRequiredInL2v1 | SBML Level 2 Version 1 requires strict unit consistency | N | N | N | N | N | W | W |
IntegerSpatialDimensions | SBML Level 2 Version 1 requires that compartments have spatial dimensions of 0-3 | N | N | N | N | N | N | E |
StoichiometryMathNotYetSupported | Conversion to StoichiometryMath objects not yet supported | N | N | N | N | N | N | N |
PriorityLostFromL3 | SBML Level 2 Version 1 does not support priorities on Event objects | N | N | N | N | N | N | E |
NonPersistentNotSupported | SBML Level 2 Version 1 does not support the 'persistent' attribute on Trigger objects | N | N | N | N | N | N | E |
InitialValueFalseEventNotSupported | SBML Level 2 Version 1 does not support the 'initialValue' attribute on Trigger objects | N | N | N | N | N | N | E |
SBOTermNotUniversalInL2v2 | The 'sboTerm' attribute is invalid for this component in SBML Level 2 Version 2 | N | N | N | N | W | W | W |
NoUnitOffsetInL2v2 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | N | N | E | N | N | N | N |
NoKineticLawTimeUnitsInL2v2 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoKineticLawSubstanceUnitsInL2v2 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoDelayedEventAssignmentInL2v2 | This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute | N | N | N | N | N | E | E |
ModelSBOBranchChangedBeyondL2v2 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | N | N | N | N | N | E | E |
StrictUnitsRequiredInL2v2 | SBML Level 2 Version 2 requires strict unit consistency | N | N | N | N | N | W | W |
StrictSBORequiredInL2v2 | SBML Level 2 Version 2 requires strict SBO term consistency | N | N | N | N | N | W | W |
DuplicateAnnotationInvalidInL2v2 | Duplicate top-level annotations are invalid in SBML Level 2 Version 2 | W | W | W | N | N | N | N |
NoUnitOffsetInL2v3 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | N | N | E | N | N | N | N |
NoKineticLawTimeUnitsInL2v3 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoKineticLawSubstanceUnitsInL2v3 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoSpeciesSpatialSizeUnitsInL2v3 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | N | N | E | E | N | N | N |
NoEventTimeUnitsInL2v3 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | N | N | E | E | N | N | N |
NoDelayedEventAssignmentInL2v3 | This Level+Version of SBML does not support the 'useValuesFromTriggerTime' attribute | N | N | N | N | N | E | E |
ModelSBOBranchChangedBeyondL2v3 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | N | N | N | N | N | E | E |
StrictUnitsRequiredInL2v3 | SBML Level 2 Version 3 requires strict unit consistency | N | N | N | N | N | W | W |
StrictSBORequiredInL2v3 | SBML Level 2 Version 3 requires strict SBO term consistency | N | N | N | N | N | W | W |
DuplicateAnnotationInvalidInL2v3 | Duplicate top-level annotations are invalid in SBML Level 2 Version 3 | W | W | W | N | N | N | N |
NoUnitOffsetInL2v4 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | N | N | E | N | N | N | N |
NoKineticLawTimeUnitsInL2v4 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoKineticLawSubstanceUnitsInL2v4 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoSpeciesSpatialSizeUnitsInL2v4 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | N | N | E | E | N | N | N |
NoEventTimeUnitsInL2v4 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | N | N | E | E | N | N | N |
ModelSBOBranchChangedInL2v4 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | N | N | N | E | E | N | N |
DuplicateAnnotationInvalidInL2v4 | Duplicate top-level annotations are invalid in SBML Level 2 Version 4 | W | W | W | N | N | N | N |
NoSpeciesTypeInL3v1 | SBML Level 3 Version 1 does not support SpeciesType objects | N | N | N | W | W | W | N |
NoCompartmentTypeInL3v1 | SBML Level 3 Version 1 does not support CompartmentType objects | N | N | N | W | W | W | N |
NoUnitOffsetInL3v1 | This Level+Version of SBML does not support the 'offset' attribute on Unit objects | N | N | E | N | N | N | N |
NoKineticLawTimeUnitsInL3v1 | This Level+Version of SBML does not support the 'timeUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoKineticLawSubstanceUnitsInL3v1 | This Level+Version of SBML does not support the 'substanceUnits' attribute on KineticLaw objects | E | E | E | N | N | N | N |
NoSpeciesSpatialSizeUnitsInL3v1 | This Level+Version of SBML does not support the 'spatialSizeUnit' attribute on Species objects | N | N | E | E | N | N | N |
NoEventTimeUnitsInL3v1 | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | N | N | E | E | N | N | N |
ModelSBOBranchChangedInL3v1 | The allowable 'sboTerm' attribute values for Model objects differ for this SBML Level+Version | N | N | N | E | E | N | N |
DuplicateAnnotationInvalidInL3v1 | Duplicate top-level annotations are invalid in SBML Level 3 Version 1 | W | W | W | N | N | N | N |
NoCompartmentOutsideInL3v1 | This Level+Version of SBML does not support the 'outside' attribute on Compartment objects | W | W | W | W | W | W | N |
NoStoichiometryMathInL3v1 | This Level+Version of SBML does not support the StoichiometryMath object | N | N | E | E | E | E | N |
InvalidSBMLLevelVersion | Unknown Level+Version combination of SBML | E | E | E | E | E | E | E |
AnnotationNotesNotAllowedLevel1 | Annotation objects on the SBML container element are not permitted in SBML Level 1 | E | E | N | N | N | N | N |
InvalidRuleOrdering | Invalid ordering of rules | E | E | E | N | N | N | N |
RequiredPackagePresent | The SBML document requires an SBML Level 3 package unavailable in this software | N | N | N | N | N | N | E |
UnrequiredPackagePresent | The SBML document uses an SBML Level 3 package unavailable in this software | N | N | N | N | N | N | W |
PackageRequiredShouldBeFalse | This package expects required to be false. | N | N | N | N | N | N | W |
SubsUnitsAllowedInKL | Disallowed value for attribute 'substanceUnits' on KineticLaw object | E | E | E | N | N | N | N |
TimeUnitsAllowedInKL | Disallowed value for attribute 'timeUnits' on KineticLaw object | E | E | E | N | N | N | N |
FormulaInLevel1KL | Only predefined functions are allowed in SBML Level 1 formulas | E | E | N | N | N | N | N |
L3SubstanceUnitsOnModel | Invalid 'substanceUnits' attribute value | N | N | N | N | N | N | W |
TimeUnitsRemoved | This Level+Version of SBML does not support the 'timeUnits' attribute on Event objects | N | N | N | N | E | E | E |
BadMathML | Invalid MathML expression | N | N | E | E | E | E | E |
FailedMathMLReadOfDouble | Missing or invalid floating-point number in MathML expression | N | N | E | E | E | E | E |
FailedMathMLReadOfInteger | Missing or invalid integer in MathML expression | N | N | E | E | E | E | E |
FailedMathMLReadOfExponential | Missing or invalid exponential expression in MathML | N | N | E | E | E | E | E |
FailedMathMLReadOfRational | Missing or invalid rational expression in MathML | N | N | E | E | E | E | E |
BadMathMLNodeType | Invalid MathML element | N | N | E | E | E | E | E |
NoTimeSymbolInFunctionDef | Use of <csymbol> for 'time' not allowed within FunctionDefinition objects | N | N | W | E | E | E | E |
NoBodyInFunctionDef | There must be a <lambda> body within the <math> element of a FunctionDefinition object | N | N | E | E | E | E | E |
DanglingUnitSIdRef | Units must refer to valid unit or unitDefinition | W | W | W | W | W | W | W |
RDFMissingAboutTag | RDF missing the <about> tag. | N | N | N | W | W | W | W |
RDFEmptyAboutTag | RDF empty <about> tag. | N | N | N | W | W | W | W |
RDFAboutTagNotMetaid | RDF <about> tag is not metaid. | N | N | N | W | W | W | W |
RDFNotCompleteModelHistory | RDF does not contain valid ModelHistory. | N | N | N | W | W | W | W |
RDFNotModelHistory | RDF does not result in a ModelHistory. | N | N | N | W | W | W | W |
AnnotationNotElement | Annotation must contain element. | N | N | N | W | W | W | W |
UndeclaredUnits | Missing unit declarations on parameters or literal numbers in expression | W | W | W | W | W | W | W |
UndeclaredTimeUnitsL3 | Unable to verify consistency of units: the unit of time has not been declared | N | N | N | N | N | N | W |
UndeclaredExtentUnitsL3 | Unable to verify consistency of units: the units of reaction extent have not been declared | N | N | N | N | N | N | W |
UndeclaredObjectUnitsL3 | Unable to verify consistency of units: encountered a model entity with no declared units | N | N | N | N | N | N | W |
UnrecognisedSBOTerm | Unrecognized 'sboTerm' attribute value | N | N | N | W | W | W | W |
ObseleteSBOTerm | Obsolete 'sboTerm' attribute value | N | N | N | W | W | W | W |
IncorrectCompartmentSpatialDimensions | In SBML Level 1, only three-dimensional compartments are allowed | E | E | N | N | N | N | N |
CompartmentTypeNotValidAttribute | CompartmentType objects are not available in this Level+Version of SBML | E | E | E | N | N | N | E |
ConstantNotValidAttribute | This Level+Version of SBML does not support the 'constant' attribute on this component | E | E | N | N | N | N | N |
MetaIdNotValidAttribute | Attribute 'metaid' is not available in SBML Level 1 | E | E | N | N | N | N | N |
SBOTermNotValidAttributeBeforeL2V3 | The 'sboTerm' attribute is not available on this component before SBML Level 2 Version 3 | E | E | E | E | N | N | N |
InvalidL1CompartmentUnits | Invalid units for a compartment in SBML Level 1 | E | E | N | N | N | N | N |
L1V1CompartmentVolumeReqd | In SBML Level 1, a compartment's volume must be specified | E | N | N | N | N | N | N |
CompartmentTypeNotValidComponent | CompartmentType objects are not available in this Level+Version of SBML | E | E | E | N | N | N | E |
ConstraintNotValidComponent | Constraint objects are not available in this Level+Version of SBML | E | E | E | N | N | N | N |
EventNotValidComponent | Event objects are not available in this Level+Version of SBML | E | E | N | N | N | N | N |
SBOTermNotValidAttributeBeforeL2V2 | The 'sboTerm' attribute is invalid for this component before Level 2 Version 2 | E | E | E | N | N | N | N |
FuncDefNotValidComponent | FunctionDefinition objects are not available in this Level+Version of SBML | E | E | N | N | N | N | N |
InitialAssignNotValidComponent | InitialAssignment objects are not available in this Level+Version of SBML | E | E | E | N | N | N | N |
VariableNotValidAttribute | Attribute 'variable' is not available on this component in this Level+Version of SBML | E | E | E | E | E | E | E |
UnitsNotValidAttribute | Attribute 'units' is not available on this component in this Level+Version of SBML | E | E | E | E | E | E | E |
ConstantSpeciesNotValidAttribute | Attribute 'constant' is not available on Species objects in SBML Level 1 | E | E | N | N | N | N | N |
SpatialSizeUnitsNotValidAttribute | Attribute 'spatialSizeUnits' is not available on Species objects in SBML Level 1 | E | E | N | N | N | N | N |
SpeciesTypeNotValidAttribute | Attribute 'speciesType' is not available on Species objects in SBML Level 1 | E | E | E | N | N | N | E |
HasOnlySubsUnitsNotValidAttribute | Attribute 'hasOnlySubstanceUnits' is not available on Species objects in SBML Level 1 | E | E | N | N | N | N | N |
IdNotValidAttribute | Attribute 'id' is not available on SpeciesReference objects in SBML Level 1 | E | E | E | N | N | N | N |
NameNotValidAttribute | Attribute 'name' is not available on SpeciesReference objects in SBML Level 1 | E | E | E | N | N | N | N |
SpeciesTypeNotValidComponent | The SpeciesType object is not supported in SBML Level 1 | E | E | E | N | N | N | E |
StoichiometryMathNotValidComponent | The StoichiometryMath object is not supported in SBML Level 1 | E | E | N | N | N | N | E |
MultiplierNotValidAttribute | Attribute 'multiplier' on Unit objects is not supported in SBML Level 1 | E | E | N | N | N | N | N |
OffsetNotValidAttribute | Attribute 'offset' on Unit objects is only available in SBML Level 2 Version 1 | E | E | N | N | N | N | N |
L3SpatialDimensionsUnset | No value given for 'spatialDimensions' attribute; assuming a value of 3 | N | N | N | N | N | N | W |
PackageConversionNotSupported | Conversion of SBML Level 3 package constructs is not yet supported | E | E | E | E | E | E | E |
InvalidTargetLevelVersion | The requested SBML Level/Version combination is not known to exist | E | E | E | E | E | E | E |
L3NotSupported | SBML Level 3 is not yet supported | E | E | E | E | E | E | E |
CompUnknown | Unknown error from comp | N | N | N | N | N | N | E |
CompNSUndeclared | The comp ns is not correctly declared | N | N | N | N | N | N | E |
CompElementNotInNs | Element not in comp namespace | N | N | N | N | N | N | E |
CompDuplicateComponentId | Duplicate 'id' attribute value | N | N | N | N | N | N | E |
CompUniqueModelIds | Model and ExternalModelDefinitions must have unique ids | N | N | N | N | N | N | E |
CompUniquePortIds | Ports must have unique ids | N | N | N | N | N | N | E |
CompInvalidSIdSyntax | Invalid SId syntax | N | N | N | N | N | N | E |
CompInvalidSubmodelRefSyntax | Invalid submodelRef syntax | N | N | N | N | N | N | E |
CompInvalidDeletionSyntax | Invalid deletion syntax | N | N | N | N | N | N | E |
CompInvalidConversionFactorSyntax | Invalid conversionFactor syntax | N | N | N | N | N | N | E |
CompInvalidNameSyntax | Invalid name syntax | N | N | N | N | N | N | E |
CompReplacedUnitsShouldMatch | Units of replaced elements should match replacement units. | N | N | N | N | N | N | W |
CompOneListOfReplacedElements | Only one <listOfReplacedElements> allowed. | N | N | N | N | N | N | E |
CompLOReplaceElementsAllowedElements | Allowed children of <listOfReplacedElements> | N | N | N | N | N | N | E |
CompLOReplacedElementsAllowedAttribs | Allowed <listOfReplacedElements> attributes | N | N | N | N | N | N | E |
CompEmptyLOReplacedElements | <listOfReplacedElements> must not be empty | N | N | N | N | N | N | E |
CompOneReplacedByElement | Only one <replacedBy> object allowed. | N | N | N | N | N | N | E |
CompAttributeRequiredMissing | Required comp:required attribute on <sbml> | N | N | N | N | N | N | E |
CompAttributeRequiredMustBeBoolean | The comp:required attribute must be Boolean | N | N | N | N | N | N | E |
CompRequiredTrueIfElementsRemain | The comp:required attribute must be 'true' if math changes. NOTE: Deprecated | N | N | N | N | N | N | E |
CompRequiredFalseIfAllElementsReplaced | The comp:required attribute must be 'false' if math does not change. NOTE: Deprecated | N | N | N | N | N | N | E |
CompOneListOfModelDefinitions | Only one <listOfModelDefinitions> allowed. | N | N | N | N | N | N | E |
CompEmptyLOModelDefs | <listOfModelDefinitions> and <listOfExternalModelDefinitions> must not be empty | N | N | N | N | N | N | E |
CompLOModelDefsAllowedElements | Only <modelDefinitions> in <listOfModelDefinitions> | N | N | N | N | N | N | E |
CompLOExtModelDefsAllowedElements | Only <externalModelDefinitions> in <listOfExternalModelDefinitions> | N | N | N | N | N | N | E |
CompLOModelDefsAllowedAttributes | Allowed <listOfModelDefinitions> attributes | N | N | N | N | N | N | E |
CompLOExtModDefsAllowedAttributes | Allowed <listOfExternalModelDefinitions> attributes | N | N | N | N | N | N | E |
CompOneListOfExtModelDefinitions | Only one <listOfExternalModelDefinitions> allowed. | N | N | N | N | N | N | E |
CompAttributeRequiredMustBeTrue | The comp:required attribute must be 'true' | N | N | N | N | N | N | E |
CompExtModDefAllowedCoreAttributes | Allowed <externalModelDefinitions> core attributes | N | N | N | N | N | N | E |
CompExtModDefAllowedElements | Allowed <externalModelDefinitions> elements | N | N | N | N | N | N | E |
CompExtModDefAllowedAttributes | Allowed <externalModelDefinitions> attributes | N | N | N | N | N | N | E |
CompReferenceMustBeL3 | External models must be L3 | N | N | N | N | N | N | E |
CompModReferenceMustIdOfModel | 'modelRef' must be the 'id' of a model in the 'source' document | N | N | N | N | N | N | E |
CompExtModMd5DoesNotMatch | MD5 checksum does not match the 'source' document | N | N | N | N | N | N | W |
CompInvalidSourceSyntax | The 'comp:source' attribute must be of type 'anyURI' | N | N | N | N | N | N | E |
CompInvalidModelRefSyntax | The 'comp:modelRef' attribute must have the syntax of 'SId' | N | N | N | N | N | N | E |
CompInvalidMD5Syntax | The 'comp:md5' attribute must have the syntax of 'string' | N | N | N | N | N | N | E |
CompCircularExternalModelReference | Circular reference in <externalModelDefinitiongt; | N | N | N | N | N | N | E |
CompOneListOfOnModel | Only one <listOfSubmodels> and one <listOfPorts> allowed | N | N | N | N | N | N | E |
CompNoEmptyListOfOnModel | No empty listOf elements allowed | N | N | N | N | N | N | E |
CompLOSubmodelsAllowedElements | Allowed elements on <listOfSubmodels> | N | N | N | N | N | N | E |
CompLOPortsAllowedElements | Allowed elements on <listOfPorts> | N | N | N | N | N | N | E |
CompLOSubmodelsAllowedAttributes | Allowed attributes on <listOfSubmodels> | N | N | N | N | N | N | E |
CompLOPortsAllowedAttributes | Allowed attributes on <listOfPorts> | N | N | N | N | N | N | E |
CompSubmodelAllowedCoreAttributes | Allowed core attributes on <submodel> | N | N | N | N | N | N | E |
CompSubmodelAllowedElements | Allowed elements on <submodel> | N | N | N | N | N | N | E |
CompOneListOfDeletionOnSubmodel | Only one <listOfDeletions> on a <submodel> allowed | N | N | N | N | N | N | E |
CompSubmodelNoEmptyLODeletions | No empty listOfDeletions elements allowed | N | N | N | N | N | N | E |
CompLODeletionsAllowedElements | Allowed elements on <listOfDeletions> | N | N | N | N | N | N | E |
CompLODeletionAllowedAttributes | Allowed <listOfDeletions> attributes | N | N | N | N | N | N | E |
CompSubmodelAllowedAttributes | Allowed <submodel> attributes | N | N | N | N | N | N | E |
CompModReferenceSyntax | 'comp:modelRef' must conform to SId syntax | N | N | N | N | N | N | E |
CompInvalidTimeConvFactorSyntax | 'comp:timeConversionFactor' must conform to SId syntax | N | N | N | N | N | N | E |
CompInvalidExtentConvFactorSyntax | 'comp:extentConversionFactor' must conform to SId syntax | N | N | N | N | N | N | E |
CompSubmodelMustReferenceModel | The 'comp:modelRef' attribute must reference a model | N | N | N | N | N | N | E |
CompSubmodelCannotReferenceSelf | The 'comp:modelRef' attribute cannot reference own model | N | N | N | N | N | N | E |
CompModCannotCircularlyReferenceSelf | <model> may not reference <submodel> that references itself. | N | N | N | N | N | N | E |
CompTimeConversionMustBeParameter | The 'comp:timeConversionFactor' must reference a parameter | N | N | N | N | N | N | E |
CompExtentConversionMustBeParameter | The 'comp:extentConversionFactor' must reference a parameter | N | N | N | N | N | N | E |
CompPortRefMustReferencePort | The 'comp:portRef' attribute must be the 'id' of a <port> | N | N | N | N | N | N | E |
CompIdRefMustReferenceObject | The 'comp:idRef' attribute must be the 'id' of a model element | N | N | N | N | N | N | E |
CompUnitRefMustReferenceUnitDef | The 'comp:unitRef' attribute must be the 'id' of a UnitDefinition | N | N | N | N | N | N | E |
CompMetaIdRefMustReferenceObject | The 'comp:metaIdRef' attribute must be the 'metaid' of an object | N | N | N | N | N | N | E |
CompParentOfSBRefChildMustBeSubmodel | If <sBaseRef> has a child <sBaseRef> its parent must be a <submodel> | N | N | N | N | N | N | E |
CompInvalidPortRefSyntax | The 'comp:portRef' attribute must have the syntax of an SBML SId | N | N | N | N | N | N | E |
CompInvalidIdRefSyntax | The 'comp:idRef' attribute must have the syntax of an SBML SId | N | N | N | N | N | N | E |
CompInvalidUnitRefSyntax | The 'comp:unitRef' attribute must have the syntax of an SBML SId | N | N | N | N | N | N | E |
CompInvalidMetaIdRefSyntax | The 'comp:metaIdRef' attribute must have the syntax of an XML ID | N | N | N | N | N | N | E |
CompOneSBaseRefOnly | Only one <sbaseRef> | N | N | N | N | N | N | E |
CompDeprecatedSBaseRefSpelling | The spelling 'sbaseRef' is deprecated | N | N | N | N | N | N | W |
CompSBaseRefMustReferenceObject | An SBaseRef must reference an object. | N | N | N | N | N | N | E |
CompSBaseRefMustReferenceOnlyOneObject | An SBaseRef must reference only one other object. | N | N | N | N | N | N | E |
CompNoMultipleReferences | Objects may not be referenced by multiple SBaseRef constructs. | N | N | N | N | N | N | E |
CompPortMustReferenceObject | Port must reference an object | N | N | N | N | N | N | E |
CompPortMustReferenceOnlyOneObject | Port must reference only one other object. | N | N | N | N | N | N | E |
CompPortAllowedAttributes | Allowed attributes on a Port | N | N | N | N | N | N | E |
CompPortReferencesUnique | Port definitions must be unique. | N | N | N | N | N | N | E |
CompDeletionMustReferenceObject | Deletion must reference an object | N | N | N | N | N | N | E |
CompDeletionMustReferOnlyOneObject | Deletion must reference only one other object. | N | N | N | N | N | N | E |
CompDeletionAllowedAttributes | Allowed attributes on a Deletion | N | N | N | N | N | N | E |
CompReplacedElementMustRefObject | ReplacedElement must reference an object | N | N | N | N | N | N | E |
CompReplacedElementMustRefOnlyOne | ReplacedElement must reference only one other object. | N | N | N | N | N | N | E |
CompReplacedElementAllowedAttributes | Allowed attributes on <replacedElement> | N | N | N | N | N | N | E |
CompReplacedElementSubModelRef | The 'comp:submodelRef' attribute must point to a <submodel> | N | N | N | N | N | N | E |
CompReplacedElementDeletionRef | The 'comp:deletion' attribute must point to a <deletion> | N | N | N | N | N | N | E |
CompReplacedElementConvFactorRef | The 'comp:conversionFactor attribute must point to a <parameter> | N | N | N | N | N | N | E |
CompReplacedElementSameReference | No <replacedElement> refer to same object | N | N | N | N | N | N | E |
CompReplacedElementNoDelAndConvFact | No <replacedElement> with deletion and conversionfactor | N | N | N | N | N | N | E |
CompReplacedByMustRefObject | ReplacedBy must reference an object | N | N | N | N | N | N | E |
CompReplacedByMustRefOnlyOne | ReplacedBy must reference only one other object. | N | N | N | N | N | N | E |
CompReplacedByAllowedAttributes | Allowed attributes on <replacedBy> | N | N | N | N | N | N | E |
CompReplacedBySubModelRef | The 'comp:submodelRef' attribute must point to a <submodel> | N | N | N | N | N | N | E |
CompMustReplaceSameClass | Replaced classes must match. | N | N | N | N | N | N | E |
CompMustReplaceIDs | Replaced IDs must be replaced with IDs. | N | N | N | N | N | N | E |
CompMustReplaceMetaIDs | Replaced metaids must be replaced with metaids. | N | N | N | N | N | N | E |
CompMustReplacePackageIDs | Replaced package IDs must be replaced with package IDs. | N | N | N | N | N | N | E |
CompUnresolvedReference | Unresolved reference. | N | N | N | N | N | N | E |
CompNoModelInReference | No model in referenced document. | N | N | N | N | N | N | E |
CompExtModDefBad | Referenced <externalModelDefinitiongt; unresolvable. | N | N | N | N | N | N | E |
CompModelFlatteningFailed | Model failed to flatten. | N | N | N | N | N | N | E |
CompFlatModelNotValid | Flat model not valid. | N | N | N | N | N | N | E |
CompLineNumbersUnreliable | Line numbers unreliable. | N | N | N | N | N | N | W |
CompFlatteningNotRecognisedReqd | Flattening not implemented for required package. | N | N | N | N | N | N | W |
CompFlatteningNotRecognisedNotReqd | Flattening not implemented for unrequired package. | N | N | N | N | N | N | W |
CompFlatteningNotImplementedNotReqd | Flattening not implemented for unrequired package. | N | N | N | N | N | N | W |
CompFlatteningNotImplementedReqd | Flattening not implemented for required package. | N | N | N | N | N | N | W |
CompFlatteningWarning | Flattening reference may come from package. | N | N | N | N | N | N | W |
CompDeprecatedDeleteFunction | The performDeletions functions is deprecated. | N | N | N | N | N | N | E |
CompDeprecatedReplaceFunction | The performReplacementsAndConversions functions is deprecated. | N | N | N | N | N | N | E |
CompDeletedReplacement | Element deleted before a subelement could be replaced. | N | N | N | N | N | N | E |
CompIdRefMayReferenceUnknownPackage | The 'comp:idRef' attribute must be the 'id' of a model element | N | N | N | N | N | N | W |
CompMetaIdRefMayReferenceUnknownPkg | The 'comp:metaIdRef' attribute must be the 'metaid' of a model element | N | N | N | N | N | N | W |
FbcUnknown | Unknown error from fbc | N | N | N | N | N | N | E |
FbcNSUndeclared | The fbc ns is not correctly declared | N | N | N | N | N | N | E |
FbcElementNotInNs | Element not in fbc namespace | N | N | N | N | N | N | E |
FbcDuplicateComponentId | Duplicate 'id' attribute value | N | N | N | N | N | N | E |
FbcSBMLSIdSyntax | Invalid 'id' attribute | N | N | N | N | N | N | E |
FbcAttributeRequiredMissing | Required fbc:required attribute on <sbml> | N | N | N | N | N | N | E |
FbcAttributeRequiredMustBeBoolean | The fbc:required attribute must be Boolean | N | N | N | N | N | N | E |
FbcRequiredFalse | The fbc:required attribute must be 'false' | N | N | N | N | N | N | E |
FbcOnlyOneEachListOf | One of each list of allowed | N | N | N | N | N | N | E |
FbcNoEmptyListOfs | ListOf elements cannot be empty | N | N | N | N | N | N | E |
FbcLOFluxBoundsAllowedElements | Allowed elements on ListOfFluxBounds | N | N | N | N | N | N | E |
FbcLOObjectivesAllowedElements | Allowed elements on ListOfObjectives | N | N | N | N | N | N | E |
FbcLOFluxBoundsAllowedAttributes | Allowed attributes on ListOfFluxBounds | N | N | N | N | N | N | E |
FbcLOObjectivesAllowedAttributes | Allowed attributes on ListOfObjectives | N | N | N | N | N | N | E |
FbcActiveObjectiveSyntax | Type of activeObjective attribute | N | N | N | N | N | N | E |
FbcActiveObjectiveRefersObjective | ActiveObjective must reference Objective | N | N | N | N | N | N | E |
FbcSpeciesAllowedL3Attributes | Species allowed attributes | N | N | N | N | N | N | E |
FbcSpeciesChargeMustBeInteger | Charge must be integer | N | N | N | N | N | N | E |
FbcSpeciesFormulaMustBeString | Chemical formula must be string | N | N | N | N | N | N | E |
FbcFluxBoundAllowedL3Attributes | <fluxBound> may only have 'metaId' and 'sboTerm' from L3 namespace | N | N | N | N | N | N | E |
FbcFluxBoundAllowedElements | <fluxBound> may only have <notes> and <annotations> from L3 Core | N | N | N | N | N | N | E |
FbcFluxBoundRequiredAttributes | Invalid attribute found on <fluxBound> object | N | N | N | N | N | N | E |
FbcFluxBoundRectionMustBeSIdRef | Datatype for 'fbc:reaction' must be SIdRef | N | N | N | N | N | N | E |
FbcFluxBoundNameMustBeString | The attribute 'fbc:name' must be of the data type string | N | N | N | N | N | N | E |
FbcFluxBoundOperationMustBeEnum | The attribute 'fbc:operation' must be of data type FbcOperation | N | N | N | N | N | N | E |
FbcFluxBoundValueMustBeDouble | The attribute 'fbc:value' must be of the data type float | N | N | N | N | N | N | E |
FbcFluxBoundReactionMustExist | 'fbc:reaction' must refer to valid reaction | N | N | N | N | N | N | E |
FbcFluxBoundsForReactionConflict | Conflicting set of FluxBounds for a reaction | N | N | N | N | N | N | E |
FbcObjectiveAllowedL3Attributes | <objective> may only have 'metaId' and 'sboTerm' from L3 namespace | N | N | N | N | N | N | E |
FbcObjectiveAllowedElements | <objective> may only have <notes> and <annotations> from L3 Core | N | N | N | N | N | N | E |
FbcObjectiveRequiredAttributes | Invalid attribute found on <objective> object | N | N | N | N | N | N | E |
FbcObjectiveNameMustBeString | The attribute 'fbc:name' must be of the data type string | N | N | N | N | N | N | E |
FbcObjectiveTypeMustBeEnum | The attribute 'fbc:type' must be of data type FbcType. | N | N | N | N | N | N | E |
FbcObjectiveOneListOfObjectives | An <objective> must have one <listOfFluxObjectives> . | N | N | N | N | N | N | E |
FbcObjectiveLOFluxObjMustNotBeEmpty | <listOfFluxObjectives> subobject must not be empty | N | N | N | N | N | N | E |
FbcObjectiveLOFluxObjOnlyFluxObj | Invalid element found in <listOfFluxObjectives> | N | N | N | N | N | N | E |
FbcObjectiveLOFluxObjAllowedAttribs | <listOfFluxObjectives> may only have 'metaId' and 'sboTerm' from L3 core | N | N | N | N | N | N | E |
FbcFluxObjectAllowedL3Attributes | <fluxObjectivegt; may only have 'metaId' and 'sboTerm' from L3 namespace | N | N | N | N | N | N | E |
FbcFluxObjectAllowedElements | <fluxObjectivegt; may only have <notes> and <annotations> from L3 Core | N | N | N | N | N | N | E |
FbcFluxObjectRequiredAttributes | Invalid attribute found on <fluxObjectivegt; object | N | N | N | N | N | N | E |
FbcFluxObjectNameMustBeString | The attribute 'fbc:name' must be of the data type string | N | N | N | N | N | N | E |
FbcFluxObjectReactionMustBeSIdRef | Datatype for 'fbc:reaction' must be SIdRef | N | N | N | N | N | N | E |
FbcFluxObjectReactionMustExist | 'fbc:reaction' must refer to valid reaction | N | N | N | N | N | N | E |
FbcFluxObjectCoefficientMustBeDouble | The attribute 'fbc:coefficient' must be of the data type float | N | N | N | N | N | N | E |
LayoutUnknownError | Unknown error from layout | N | N | N | N | N | N | E |
LayoutNSUndeclared | The layout ns is not correctly declared | N | N | N | N | N | N | E |
LayoutElementNotInNs | Element not in layout namespace | N | N | N | N | N | N | E |
LayoutDuplicateComponentId | Duplicate 'id' attribute value | N | N | N | N | N | N | E |
LayoutSIdSyntax | 'id' attribute incorrect syntax | N | N | N | N | N | N | E |
LayoutXsiTypeAllowedLocations | 'xsi:type' allowed locations | N | N | N | N | N | N | E |
LayoutXsiTypeSyntax | 'xsi:type' attribute incorrect syntax | N | N | N | N | N | N | E |
LayoutAttributeRequiredMissing | Required layout:required attribute on <sbml> | N | N | N | N | N | N | E |
LayoutAttributeRequiredMustBeBoolean | The layout:required attribute must be Boolean | N | N | N | N | N | N | E |
LayoutRequiredFalse | The layout:required attribute must be 'false' | N | N | N | N | N | N | E |
LayoutOnlyOneLOLayouts | Only one listOfLayouts on <model> | N | N | N | N | N | N | E |
LayoutLOLayoutsNotEmpty | ListOf elements cannot be empty | N | N | N | N | N | N | E |
LayoutLOLayoutsAllowedElements | Allowed elements on ListOfLayouts | N | N | N | N | N | N | E |
LayoutLOLayoutsAllowedAttributes | Allowed attributes on ListOfLayouts | N | N | N | N | N | N | E |
LayoutLayoutAllowedElements | Allowed elements on Layout | N | N | N | N | N | N | E |
LayoutLayoutAllowedCoreAttributes | Allowed core attributes on Layout | N | N | N | N | N | N | E |
LayoutOnlyOneEachListOf | Only one each listOf on <layout> | N | N | N | N | N | N | E |
LayoutNoEmptyListOfs | ListOf elements cannot be empty | N | N | N | N | N | N | E |
LayoutLayoutAllowedAttributes | <layout> must have 'id' and may have 'name' | N | N | N | N | N | N | E |
LayoutLayoutNameMustBeString | 'name' must be string | N | N | N | N | N | N | E |
LayoutLOCompGlyphAllowedAttributes | Attributes allowed on <listOfCompartmentGlyphs> . | N | N | N | N | N | N | E |
LayoutLOCompGlyphAllowedElements | Elements allowed on <listOfCompartmentGlyphs> . | N | N | N | N | N | N | E |
LayoutLOSpeciesGlyphAllowedAttributes | Attributes allowed on <listOfSpeciesGlyphs> . | N | N | N | N | N | N | E |
LayoutLOSpeciesGlyphAllowedElements | Elements allowed on <listOfSpeciesGlyphs> . | N | N | N | N | N | N | E |
LayoutLORnGlyphAllowedAttributes | Attributes allowed on <listOfReactionGlyphs> . | N | N | N | N | N | N | E |
LayoutLORnGlyphAllowedElements | Elements allowed on <listOfReactionGlyphs> . | N | N | N | N | N | N | E |
LayoutLOAddGOAllowedAttribut | Attributes allowed on <listOfAdditionalGraphicalObjectGlyphs> . | N | N | N | N | N | N | E |
LayoutLOAddGOAllowedElements | Elements allowed on <listOfAdditionalGraphicalObjectGlyphs> . | N | N | N | N | N | N | E |
LayoutLayoutMustHaveDimensions | Layout must have <dimensions> . | N | N | N | N | N | N | E |
LayoutLOTextGlyphAllowedAttributes | Attributes allowed on <listOfTextGlyphs> . | N | N | N | N | N | N | E |
LayoutLOTextGlyphAllowedElements | Elements allowed on <listOfTextGlyphs> . | N | N | N | N | N | N | E |
LayoutGOAllowedCoreElements | Core elements allowed on <graphicalObject> . | N | N | N | N | N | N | E |
LayoutGOAllowedCoreAttributes | Core attributes allowed on <graphicalObject> . | N | N | N | N | N | N | E |
LayoutGOAllowedElements | Layout elements allowed on <graphicalObject> . | N | N | N | N | N | N | E |
LayoutGOAllowedAttributes | Layout attributes allowed on <graphicalObject> . | N | N | N | N | N | N | E |
LayoutGOMetaIdRefMustBeIDREF | Layout 'metIdRef' must be IDREF. | N | N | N | N | N | N | E |
LayoutGOMetaIdRefMustReferenceObject | Layout 'metIdRef' must reference existing object. | N | N | N | N | N | N | E |
LayoutGOMustContainBoundingBox | A <graphicalObject> must contain a <boundingBox> . | N | N | N | N | N | N | E |
LayoutCGAllowedCoreElements | Core elements allowed on <compartmentGlyph> . | N | N | N | N | N | N | E |
LayoutCGAllowedCoreAttributes | Core attributes allowed on <compartmentGlyph> . | N | N | N | N | N | N | E |
LayoutCGAllowedElements | Layout elements allowed on <compartmentGlyph> . | N | N | N | N | N | N | E |
LayoutCGAllowedAttributes | Layout attributes allowed on <compartmentGlyph> . | N | N | N | N | N | N | E |
LayoutCGMetaIdRefMustBeIDREF | Layout 'metIdRef' must be IDREF. | N | N | N | N | N | N | E |
LayoutCGMetaIdRefMustReferenceObject | Layout 'metIdRef' must reference existing object. | N | N | N | N | N | N | E |
LayoutCGCompartmentSyntax | CompartmentGlyph 'compartment' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutCGCompartmentMustRefComp | CompartmentGlyph compartment must reference existing compartment. | N | N | N | N | N | N | E |
LayoutCGNoDuplicateReferences | CompartmentGlyph cannot reference two objects. | N | N | N | N | N | N | E |
LayoutCGOrderMustBeDouble | CompartmentGlyph order must be float. | N | N | N | N | N | N | E |
LayoutSGAllowedCoreElements | Core elements allowed on <speciesGlyph> . | N | N | N | N | N | N | E |
LayoutSGAllowedCoreAttributes | Core attributes allowed on <speciesGlyph> . | N | N | N | N | N | N | E |
LayoutSGAllowedElements | Layout elements allowed on <speciesGlyph> . | N | N | N | N | N | N | E |
LayoutSGAllowedAttributes | Layout attributes allowed on <speciesGlyph> . | N | N | N | N | N | N | E |
LayoutSGMetaIdRefMustBeIDREF | Layout 'metIdRef' must be IDREF. | N | N | N | N | N | N | E |
LayoutSGMetaIdRefMustReferenceObject | Layout 'metIdRef' must reference existing object. | N | N | N | N | N | N | E |
LayoutSGSpeciesSyntax | SpeciesGlyph 'species' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutSGSpeciesMustRefSpecies | SpeciesGlyph species must reference existing species. | N | N | N | N | N | N | E |
LayoutSGNoDuplicateReferences | SpeciesGlyph cannot reference two objects. | N | N | N | N | N | N | E |
LayoutRGAllowedCoreElements | Core elements allowed on <reactionGlyph> . | N | N | N | N | N | N | E |
LayoutRGAllowedCoreAttributes | Core attributes allowed on <reactionGlyph> . | N | N | N | N | N | N | E |
LayoutRGAllowedElements | Layout elements allowed on <reactionGlyph> . | N | N | N | N | N | N | E |
LayoutRGAllowedAttributes | Layout attributes allowed on <reactionGlyph> . | N | N | N | N | N | N | E |
LayoutRGMetaIdRefMustBeIDREF | Layout 'metIdRef' must be IDREF. | N | N | N | N | N | N | E |
LayoutRGMetaIdRefMustReferenceObject | Layout 'metIdRef' must reference existing object. | N | N | N | N | N | N | E |
LayoutRGReactionSyntax | ReactionGlyph 'reaction' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutRGReactionMustRefReaction | ReactionGlyph reaction must reference existing reaction. | N | N | N | N | N | N | E |
LayoutRGNoDuplicateReferences | ReactionGlyph cannot reference two objects. | N | N | N | N | N | N | E |
LayoutLOSpeciesRefGlyphAllowedElements | Allowed elements on ListOfSpeciesReferenceGlyphs | N | N | N | N | N | N | E |
LayoutLOSpeciesRefGlyphAllowedAttribs | Allowed attributes on ListOfSpeciesReferenceGlyphs | N | N | N | N | N | N | E |
LayoutLOSpeciesRefGlyphNotEmpty | ListOfSpeciesReferenceGlyphs not empty | N | N | N | N | N | N | E |
LayoutGGAllowedCoreElements | Core elements allowed on <generalGlyph> . | N | N | N | N | N | N | E |
LayoutGGAllowedCoreAttributes | Core attributes allowed on <generalGlyph> . | N | N | N | N | N | N | E |
LayoutGGAllowedElements | Layout elements allowed on <generalGlyph> . | N | N | N | N | N | N | E |
LayoutGGAllowedAttributes | Layout attributes allowed on <generalGlyph> . | N | N | N | N | N | N | E |
LayoutGGMetaIdRefMustBeIDREF | Layout 'metIdRef' must be IDREF. | N | N | N | N | N | N | E |
LayoutGGMetaIdRefMustReferenceObject | Layout 'metIdRef' must reference existing object. | N | N | N | N | N | N | E |
LayoutGGReferenceSyntax | GeneralGlyph 'reference' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutGGReferenceMustRefObject | GeneralGlyph 'reference' must reference existing element. | N | N | N | N | N | N | E |
LayoutGGNoDuplicateReferences | GeneralGlyph cannot reference two objects. | N | N | N | N | N | N | E |
LayoutLOReferenceGlyphAllowedElements | Allowed elements on ListOfReferenceGlyphs | N | N | N | N | N | N | E |
LayoutLOReferenceGlyphAllowedAttribs | Allowed attributes on ListOfReferenceGlyphs | N | N | N | N | N | N | E |
LayoutLOSubGlyphAllowedElements | Allowed elements on ListOfSubGlyphs | N | N | N | N | N | N | E |
LayoutLOSubGlyphAllowedAttribs | Allowed attributes on ListOfSubGlyphs | N | N | N | N | N | N | E |
LayoutTGAllowedCoreElements | Core elements allowed on <textGlyph> . | N | N | N | N | N | N | E |
LayoutTGAllowedCoreAttributes | Core attributes allowed on <textGlyph> . | N | N | N | N | N | N | E |
LayoutTGAllowedElements | Layout elements allowed on <textGlyph> . | N | N | N | N | N | N | E |
LayoutTGAllowedAttributes | Layout attributes allowed on <textGlyph> . | N | N | N | N | N | N | E |
LayoutTGMetaIdRefMustBeIDREF | Layout 'metIdRef' must be IDREF. | N | N | N | N | N | N | E |
LayoutTGMetaIdRefMustReferenceObject | Layout 'metIdRef' must reference existing object. | N | N | N | N | N | N | E |
LayoutTGOriginOfTextSyntax | TextGlyph 'originOfText' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutTGOriginOfTextMustRefObject | TextGlyph 'originOfText' must reference existing element. | N | N | N | N | N | N | E |
LayoutTGNoDuplicateReferences | TextGlyph cannot reference two objects. | N | N | N | N | N | N | E |
LayoutTGGraphicalObjectSyntax | TextGlyph 'graphicalObject' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutTGGraphicalObjectMustRefObject | TextGlyph 'graphicalObject' must reference existing element. | N | N | N | N | N | N | E |
LayoutTGTextMustBeString | TextGlyph 'text' must be string. | N | N | N | N | N | N | E |
LayoutSRGAllowedCoreElements | Core elements allowed on <speciesReferenceGlyphgt; . | N | N | N | N | N | N | E |
LayoutSRGAllowedCoreAttributes | Core attributes allowed on <speciesReferenceGlyphgt; . | N | N | N | N | N | N | E |
LayoutSRGAllowedElements | Layout elements allowed on <speciesReferenceGlyphgt; . | N | N | N | N | N | N | E |
LayoutSRGAllowedAttributes | Layout attributes allowed on <speciesReferenceGlyphgt; . | N | N | N | N | N | N | E |
LayoutSRGMetaIdRefMustBeIDREF | Layout 'metIdRef' must be IDREF. | N | N | N | N | N | N | E |
LayoutSRGMetaIdRefMustReferenceObject | Layout 'metIdRef' must reference existing object. | N | N | N | N | N | N | E |
LayoutSRGSpeciesReferenceSyntax | SpeciesReferenceGlyph 'speciesReference' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutSRGSpeciesRefMustRefObject | SpeciesReferenceGlyph 'speciesReference' must reference existing element. | N | N | N | N | N | N | E |
LayoutSRGNoDuplicateReferences | SpeciesReferenceGlyph cannot reference two objects. | N | N | N | N | N | N | E |
LayoutSRGSpeciesGlyphSyntax | SpeciesReferenceGlyph 'speciesGlyph' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutSRGSpeciesGlyphMustRefObject | SpeciesReferenceGlyph 'speciesGlyph' must reference existing element. | N | N | N | N | N | N | E |
LayoutSRGRoleSyntax | SpeciesReferenceGlyph 'role' must be string from enumeration. | N | N | N | N | N | N | E |
LayoutREFGAllowedCoreElements | Core elements allowed on <referenceGlyph> . | N | N | N | N | N | N | E |
LayoutREFGAllowedCoreAttributes | Core attributes allowed on <referenceGlyph> . | N | N | N | N | N | N | E |
LayoutREFGAllowedElements | Layout elements allowed on <referenceGlyph> . | N | N | N | N | N | N | E |
LayoutREFGAllowedAttributes | Layout attributes allowed on <referenceGlyph> . | N | N | N | N | N | N | E |
LayoutREFGMetaIdRefMustBeIDREF | Layout 'metIdRef' must be IDREF. | N | N | N | N | N | N | E |
LayoutREFGMetaIdRefMustReferenceObject | Layout 'metIdRef' must reference existing object. | N | N | N | N | N | N | E |
LayoutREFGReferenceSyntax | ReferenceGlyph 'reference' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutREFGReferenceMustRefObject | ReferenceGlyph 'reference' must reference existing element. | N | N | N | N | N | N | E |
LayoutREFGNoDuplicateReferences | ReferenceGlyph cannot reference two objects. | N | N | N | N | N | N | E |
LayoutREFGGlyphSyntax | ReferenceGlyph 'glyph' must have SIdRef syntax. | N | N | N | N | N | N | E |
LayoutREFGGlyphMustRefObject | ReferenceGlyph 'glyph' must reference existing element. | N | N | N | N | N | N | E |
LayoutREFGRoleSyntax | ReferenceGlyph 'role' must be string. | N | N | N | N | N | N | E |
LayoutPointAllowedCoreElements | Core elements allowed on <point> . | N | N | N | N | N | N | E |
LayoutPointAllowedCoreAttributes | Core attributes allowed on <point> . | N | N | N | N | N | N | E |
LayoutPointAllowedAttributes | Layout attributes allowed on <point> . | N | N | N | N | N | N | E |
LayoutPointAttributesMustBeDouble | Layout 'x', 'y' and 'z' must be float. | N | N | N | N | N | N | E |
LayoutBBoxAllowedCoreElements | Core elements allowed on <boundingBox> . | N | N | N | N | N | N | E |
LayoutBBoxAllowedCoreAttributes | Core attributes allowed on <boundingBox> . | N | N | N | N | N | N | E |
LayoutBBoxAllowedElements | Layout elements allowed on <boundingBox> . | N | N | N | N | N | N | E |
LayoutBBoxAllowedAttributes | Layout attributes allowed on <boundingBox> . | N | N | N | N | N | N | E |
LayoutBBoxConsistent3DDefinition | Layout consistent dimensions on a <boundingBox> | N | N | N | N | N | N | E |
LayoutCurveAllowedCoreElements | Core elements allowed on <curve> . | N | N | N | N | N | N | E |
LayoutCurveAllowedCoreAttributes | Core attributes allowed on <curve> . | N | N | N | N | N | N | E |
LayoutCurveAllowedElements | Layout elements allowed on <curve> . | N | N | N | N | N | N | E |
LayoutCurveAllowedAttributes | Layout attributes allowed on <curve> . | N | N | N | N | N | N | E |
LayoutLOCurveSegsAllowedAttributes | Allowed attributes on ListOfCurveSegments | N | N | N | N | N | N | E |
LayoutLOCurveSegsAllowedElements | Allowed elements on ListOfCurveSegments | N | N | N | N | N | N | E |
LayoutLOCurveSegsNotEmpty | No empty ListOfCurveSegments | N | N | N | N | N | N | E |
LayoutLSegAllowedCoreElements | Core elements allowed on <lineSegment> . | N | N | N | N | N | N | E |
LayoutLSegAllowedCoreAttributes | Core attributes allowed on <lineSegment> . | N | N | N | N | N | N | E |
LayoutLSegAllowedElements | Layout elements allowed on <lineSegment> . | N | N | N | N | N | N | E |
LayoutLSegAllowedAttributes | Layout attributes allowed on <lineSegment> . | N | N | N | N | N | N | E |
LayoutCBezAllowedCoreElements | Core elements allowed on <cubicBezier> . | N | N | N | N | N | N | E |
LayoutCBezAllowedCoreAttributes | Core attributes allowed on <cubicBezier> . | N | N | N | N | N | N | E |
LayoutCBezAllowedElements | Layout elements allowed on <cubicBezier> . | N | N | N | N | N | N | E |
LayoutCBezAllowedAttributes | Layout attributes allowed on <cubicBezier> . | N | N | N | N | N | N | E |
LayoutDimsAllowedCoreElements | Core elements allowed on <dimensions> . | N | N | N | N | N | N | E |
LayoutDimsAllowedCoreAttributes | Core attributes allowed on <dimensions> . | N | N | N | N | N | N | E |
LayoutDimsAllowedAttributes | Layout attributes allowed on <dimensions> . | N | N | N | N | N | N | E |
LayoutDimsAttributesMustBeDouble | Layout 'width', 'height' and 'depth' must be float. | N | N | N | N | N | N | E |
QualUnknown | Unknown error from qual. | N | N | N | N | N | N | E |
QualNSUndeclared | The qual ns is not correctly declared. | N | N | N | N | N | N | E |
QualElementNotInNs | Element not in qual namespace. | N | N | N | N | N | N | E |
QualFunctionTermBool | FunctionTerm should return boolean. | N | N | N | N | N | N | W |
QualMathCSymbolDisallowed | CSymbol time or delay not allowed. | N | N | N | N | N | N | W |
QualDuplicateComponentId | Duplicate 'id' attribute value. | N | N | N | N | N | N | E |
QualAttributeRequiredMissing | Required qual:required attribute on <sbml> . | N | N | N | N | N | N | E |
QualAttributeRequiredMustBeBoolean | The qual:required attribute must be Boolean. | N | N | N | N | N | N | E |
QualRequiredTrueIfTransitions | The qual:required attribute must be 'true' if math changes. | N | N | N | N | N | N | E |
QualOneListOfTransOrQS | Only one <listOfTransitions> or <listOfQualitativeSpeciesgt; allowed. | N | N | N | N | N | N | E |
QualEmptyLONotAllowed | Empty <listOfTransitions> or <listOfQualitativeSpeciesgt; not allowed. | N | N | N | N | N | N | E |
QualLOTransitiondAllowedElements | Elements allowed on <listOfTransitions> . | N | N | N | N | N | N | E |
QualLOQualSpeciesAllowedElements | Elements allowed on <listOfTransitions> . | N | N | N | N | N | N | E |
QualLOQualSpeciesAllowedAttributes | Attributes allowed on <listOfQualitativeSpeciesgt; . | N | N | N | N | N | N | E |
QualLOTransitionsAllowedAttributes | Attributes allowed on <listOfTransitions> . | N | N | N | N | N | N | E |
QualQualSpeciesAllowedCoreAttributes | Core attributes allowed on <qualitativeSpeciesgt; . | N | N | N | N | N | N | E |
QualQualSpeciesAllowedElements | Elements allowed on <qualitativeSpeciesgt; . | N | N | N | N | N | N | E |
QualQualSpeciesAllowedAttributes | Attributes allowed on <qualitativeSpeciesgt; . | N | N | N | N | N | N | E |
QualConstantMustBeBool | Attribute 'constant' on <qualitativeSpeciesgt; must be boolean. | N | N | N | N | N | N | E |
QualNameMustBeString | Attribute 'name' on <qualitativeSpeciesgt; must be string. | N | N | N | N | N | N | E |
QualInitialLevelMustBeInt | Attribute 'initialLevel' on <qualitativeSpeciesgt; must be integer. | N | N | N | N | N | N | E |
QualMaxLevelMustBeInt | Attribute 'maxLevel' on <qualitativeSpeciesgt; must be integer. | N | N | N | N | N | N | E |
QualCompartmentMustReferExisting | Attribute 'compartment' on <qualitativeSpeciesgt; must reference compartment. | N | N | N | N | N | N | E |
QualInitialLevelCannotExceedMax | Attribute 'initialLevel' on <qualitativeSpeciesgt; cannot exceed maxLevel. | N | N | N | N | N | N | E |
QualConstantQSCannotBeOutput | Constant <qualitativeSpeciesgt; cannot be an Output. | N | N | N | N | N | N | E |
QualQSAssignedOnlyOnce | A <qualitativeSpeciesgt; can only be assigned once. | N | N | N | N | N | N | E |
QualInitalLevelNotNegative | Attribute 'initialLevel' on <qualitativeSpeciesgt; cannot be negative. | N | N | N | N | N | N | E |
QualMaxLevelNotNegative | Attribute 'maxLevel' on <qualitativeSpeciesgt; cannot be negative. | N | N | N | N | N | N | E |
QualTransitionAllowedCoreAttributes | Core attributes allowed on <transition> . | N | N | N | N | N | N | E |
QualTransitionAllowedElements | Elements allowed on <transition> . | N | N | N | N | N | N | E |
QualTransitionAllowedAttributes | Attributes allowed on <transition> . | N | N | N | N | N | N | E |
QualTransitionNameMustBeString | Attribute 'name' on <transition> must be string. | N | N | N | N | N | N | E |
QualTransitionLOElements | ListOf elements on <transition> . | N | N | N | N | N | N | E |
QualTransitionEmptyLOElements | ListOf elements on <transition> not empty. | N | N | N | N | N | N | E |
QualTransitionLOInputElements | Elements on <listOfInputs> . | N | N | N | N | N | N | E |
QualTransitionLOOutputElements | Elements on <listOfOutputs> . | N | N | N | N | N | N | E |
QualTransitionLOFuncTermElements | Elements on <listOfFunctionTerms> . | N | N | N | N | N | N | E |
QualTransitionLOInputAttributes | Attributes allowed on <listOfInputs> . | N | N | N | N | N | N | E |
QualTransitionLOOutputAttributes | Attributes allowed on <listOfOutputs> . | N | N | N | N | N | N | E |
QualTransitionLOFuncTermAttributes | Attributes allowed on <listOfFunctionTerms> . | N | N | N | N | N | N | E |
QualTransitionLOFuncTermExceedMax | <listOfFunctionTerms> cannot make qualitativeSpecies exceed maxLevel. | N | N | N | N | N | N | E |
QualTransitionLOFuncTermNegative | <listOfFunctionTerms> cannot make qualitativeSpecies negative. | N | N | N | N | N | N | E |
QualInputAllowedCoreAttributes | Core attributes allowed on <input> . | N | N | N | N | N | N | E |
QualInputAllowedElements | Elements allowed on <input> . | N | N | N | N | N | N | E |
QualInputAllowedAttributes | Attributes allowed on <input> . | N | N | N | N | N | N | E |
QualInputNameMustBeString | Attribute 'name' on <input> must be string. | N | N | N | N | N | N | E |
QualInputSignMustBeSignEnum | Attribute 'sign' on <input> must be enum. | N | N | N | N | N | N | E |
QualInputTransEffectMustBeInputEffect | Attribute 'transitionEffect' on <input> must be enum. | N | N | N | N | N | N | E |
QualInputThreshMustBeInteger | Attribute 'thresholdLevel' on <input> must be non negative integer. | N | N | N | N | N | N | E |
QualInputQSMustBeExistingQS | Attribute 'qualitativeSpecies' on <input> must refer to existing. | N | N | N | N | N | N | E |
QualInputConstantCannotBeConsumed | Constant <input> cannot be consumed. | N | N | N | N | N | N | E |
QualInputThreshMustBeNonNegative | Attribute 'thresholdLevel' on <input> must be non negative integer. | N | N | N | N | N | N | E |
QualOutputAllowedCoreAttributes | Core attributes allowed on <output> . | N | N | N | N | N | N | E |
QualOutputAllowedElements | Elements allowed on <output> . | N | N | N | N | N | N | E |
QualOutputAllowedAttributes | Attributes allowed on <output> . | N | N | N | N | N | N | E |
QualOutputNameMustBeString | Attribute 'name' on <output> must be string. | N | N | N | N | N | N | E |
QualOutputTransEffectMustBeOutput | Attribute 'transitionEffect' on <output> must be enum. | N | N | N | N | N | N | E |
QualOutputLevelMustBeInteger | Attribute 'outputLevel' on <output> must be non negative integer. | N | N | N | N | N | N | E |
QualOutputQSMustBeExistingQS | Attribute 'qualitativeSpecies' on <output> must refer to existing. | N | N | N | N | N | N | E |
QualOutputConstantMustBeFalse | Constant 'qualitativeSpecies' cannot be <output> . | N | N | N | N | N | N | E |
QualOutputProductionMustHaveLevel | <output> being produced must have level. | N | N | N | N | N | N | E |
QualOutputLevelMustBeNonNegative | Attribute 'outputLevel' on <output> must be non negative integer. | N | N | N | N | N | N | E |
QualDefaultTermAllowedCoreAttributes | Core attributes allowed on <defaultTerm> . | N | N | N | N | N | N | E |
QualDefaultTermAllowedElements | Elements allowed on <defaultTerm> . | N | N | N | N | N | N | E |
QualDefaultTermAllowedAttributes | Attributes allowed on <defaultTerm> . | N | N | N | N | N | N | E |
QualDefaultTermResultMustBeInteger | Attribute 'resultLevel' on <defaultTerm> must be non negative integer. | N | N | N | N | N | N | E |
QualDefaultTermResultMustBeNonNeg | Attribute 'resultLevel' on <defaultTerm> must be non negative integer. | N | N | N | N | N | N | E |
QualFuncTermAllowedCoreAttributes | Core attributes allowed on <functionTerm> . | N | N | N | N | N | N | E |
QualFuncTermAllowedElements | Elements allowed on <functionTerm> . | N | N | N | N | N | N | E |
QualFuncTermAllowedAttributes | Attributes allowed on <functionTerm> . | N | N | N | N | N | N | E |
QualFuncTermOnlyOneMath | Only one <math> on <functionTerm> . | N | N | N | N | N | N | E |
QualFuncTermResultMustBeInteger | Attribute 'resultLevel' on <functionTerm> must be non negative integer. | N | N | N | N | N | N | E |
QualFuncTermResultMustBeNonNeg | Attribute 'resultLevel' on <functionTerm> must be non negative integer.. | N | N | N | N | N | N | E |
As discussed above, each SBMLError object contains a value for a category identifier, describing the type of issue that the SBMLError object represents. The category can be retrieved from an SBMLError object using the method SBMLError.getCategory(). The following table lists each possible value and a brief description of its meaning.
As is the case with the error codes, in the libSBML Python language interface, the category identifiers are currently implemented as static integer constants defined in the interface class libsbml.
The following table lists each possible value and a brief description of its meaning.
Enumerator | Meaning |
---|---|
LIBSBML_CAT_SBML | General error not falling into another category below. |
LIBSBML_CAT_SBML_L1_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model from SBML Level 2 to SBML Level 1. |
LIBSBML_CAT_SBML_L2V1_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 1. |
LIBSBML_CAT_SBML_L2V2_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 2. |
LIBSBML_CAT_GENERAL_CONSISTENCY | Category of errors that can occur while validating general SBML constructs. With respect to the SBML specification, these concern failures in applying the validation rules numbered 2xxxx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications. |
LIBSBML_CAT_IDENTIFIER_CONSISTENCY | Category of errors that can occur while validating symbol identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 103xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications. |
LIBSBML_CAT_UNITS_CONSISTENCY | Category of errors that can occur while validating the units of measurement on quantities in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 105xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications. |
LIBSBML_CAT_MATHML_CONSISTENCY | Category of errors that can occur while validating MathML formulas in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 102xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications. |
LIBSBML_CAT_SBO_CONSISTENCY | Category of errors that can occur while validating SBO identifiers in a model. With respect to the SBML specification, these concern failures in applying the validation rules numbered 107xx in the Level 2 Versions 2–4 and Level 3 Version 1 specifications. |
LIBSBML_CAT_OVERDETERMINED_MODEL | Error in the system of equations in the model: the system is overdetermined, therefore violating a tenet of proper SBML. With respect to the SBML specification, this is validation rule #10601 in the SBML Level 2 Versions 2–4 and Level 3 Version 1 specifications. |
LIBSBML_CAT_SBML_L2V3_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 3. |
LIBSBML_CAT_MODELING_PRACTICE | Category of warnings about recommended good practices involving SBML and computational modeling. (These are tests performed by libSBML and do not have equivalent SBML validation rules.) |
LIBSBML_CAT_INTERNAL_CONSISTENCY | Category of errors that can occur while validating libSBML's internal representation of SBML constructs. (These are tests performed by libSBML and do not have equivalent SBML validation rules.) |
LIBSBML_CAT_SBML_L2V4_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 2 Version 4. |
LIBSBML_CAT_SBML_L3V1_COMPAT | Category of errors that can only occur during attempted translation from one Level/Version of SBML to another. This particular category applies to errors encountered while trying to convert a model to SBML Level 3 Version 1. |
In libSBML version 5.10.0
there are no additional severity codes beyond those defined by XMLError. They are implemented as static integer constants defined in the interface class libsbml, and have names beginning with LIBSBML_SEV_
.
Public Member Functions | |
def | getCategory |
def | getCategoryAsString |
def | getColumn |
def | getErrorId |
def | getErrorIdOffset |
def | getLine |
def | getMessage |
def | getPackage |
def | getSeverity |
def | getSeverityAsString |
def | getShortMessage |
def | getStandardMessage |
def | isError |
def | isFatal |
def | isInfo |
def | isInternal |
def | isSystem |
def | isValid |
def | isWarning |
def | isXML |
def | setColumn |
def | setLine |
|
inherited |
Python method signature(s):
getCategory(XMLError self)long
Returns the category of this error.
XMLError defines an enumeration of category codes for the XML layer. Applications that build on XMLError by subclassing it may add their own categories with numbers higher than those in the predefined set of category codes.
Categories can be used to partition errors into distinct groups. Among other things, this can be used to prevent id conflicts by uniquely identifying an XMLError by both id and category.
|
inherited |
Python method signature(s):
getCategoryAsString(XMLError self)string
Returns a string describing the category of this error.
XMLError defines an enumeration of category codes for the XML layer. Applications that build on XMLError by subclassing it may add their own categories with numbers higher than those in the predefined set of category codes.
Categories can be used to partition errors into distinct groups. Among other things, this can be used to prevent id conflicts by uniquely identifying an XMLError by both id and category.
|
inherited |
Python method signature(s):
getColumn(XMLError self)long
Returns the column number in the XML input near where the error, warning or other diagnostic occurred.
We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0
or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.
|
inherited |
{core}
Representation of errors, warnings and other diagnosticsThis class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. This class is not prescribed by the SBML specifications, although it is used to implement features defined in SBML.
LibSBML can be configured to use any of a number of XML parsers; at the time of this writing, libSBML supports Xerces versions 2.4 through 3.1, Expat version 1.95.x and higher, and libxml2 version 2.6.16 and higher. These parsers each report different status codes for the various exceptions that can occur during XML processing. The XMLError object class abstracts away from the particular diagnostics reported by the different parsers and presents a single uniform interface and set of status codes, along with operations for manipulating the error objects.
When the libSBML XML parser layer encounters an error in the XML content being processed, or when there is something else wrong (such as an out-of-memory condition), the problems are reported as XMLError objects. Each XMLError object instance has an identification number that identifies the nature of the problem. This error identifier is one of the constants listed in the next section below. Applications can use the error identifiers as a means of recognizing the error encountered and changing their behavior if desired.
Integer error codes are useful for software, but not so much for telling humans what happened. For this reason, XMLError also provides two text messages describing the nature of the error. These messages are accessible by means of the methods XMLError.getShortMessage() and XMLError.getMessage(). The method XMLError.getShortMessage() returns a very brief synopsis of the warning or error condition, whereas XMLError.getMessage() returns a longer explanation. These text strings are suitable for displaying to human users.
Each XMLError object also contains a category code; its value may be retrieved using the method XMLError.getCategory(). Category values are drawn from a set of constants whose names begin with the characters LIBSBML_CAT_
, described below. Categories are used by libSBML to provide more information to calling programs about the nature of a given error.
In addition to category codes, each XMLError object also has a severity code; its value may be retrieved using the method XMLError.getSeverity(). Severity code values are drawn from a set of constants whose names begin with the characters LIBSBML_SEV_
, described below. Severity levels range from informational (LIBSBML_SEV_INFO) to fatal errors (LIBSBML_SEV_FATAL).
Finally, XMLError objects record the line and column near where the problem occurred in the XML content. The values can be retrieved using the methods XMLError.getLine() and XMLError.getColumn(). We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0
or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.
Enumerator | Meaning | Category | Severity |
---|---|---|---|
XMLUnknownError | Unrecognized error encountered internally | INTERNAL | FATAL |
XMLOutOfMemory | Out of memory | SYSTEM | FATAL |
XMLFileUnreadable | File unreadable | SYSTEM | ERROR |
XMLFileUnwritable | File unwritable | SYSTEM | ERROR |
XMLFileOperationError | Error encountered while attempting file operation | SYSTEM | ERROR |
XMLNetworkAccessError | Network access error | SYSTEM | ERROR |
InternalXMLParserError | Internal XML parser state error | INTERNAL | FATAL |
UnrecognizedXMLParserCode | XML parser returned an unrecognized error code | INTERNAL | FATAL |
XMLTranscoderError | Character transcoder error | INTERNAL | FATAL |
MissingXMLDecl | Missing XML declaration at beginning of XML input | XML | ERROR |
MissingXMLEncoding | Missing encoding attribute in XML declaration | XML | ERROR |
BadXMLDecl | Invalid or unrecognized XML declaration or XML encoding | XML | ERROR |
BadXMLDOCTYPE | Invalid, malformed or unrecognized XML DOCTYPE declaration | XML | ERROR |
InvalidCharInXML | Invalid character in XML content | XML | ERROR |
BadlyFormedXML | XML content is not well-formed | XML | ERROR |
UnclosedXMLToken | Unclosed XML token | XML | ERROR |
InvalidXMLConstruct | XML construct is invalid or not permitted | XML | ERROR |
XMLTagMismatch | Element tag mismatch or missing tag | XML | ERROR |
DuplicateXMLAttribute | Duplicate XML attribute | XML | ERROR |
UndefinedXMLEntity | Undefined XML entity | XML | ERROR |
BadProcessingInstruction | Invalid, malformed or unrecognized XML processing instruction | XML | ERROR |
BadXMLPrefix | Invalid or undefined XML namespace prefix | XML | ERROR |
BadXMLPrefixValue | Invalid XML namespace prefix value | XML | ERROR |
MissingXMLRequiredAttribute | Missing a required XML attribute | XML | ERROR |
XMLAttributeTypeMismatch | Data type mismatch for the value of an attribute | XML | ERROR |
XMLBadUTF8Content | Invalid UTF8 content | XML | ERROR |
MissingXMLAttributeValue | Missing or improperly formed attribute value | XML | ERROR |
BadXMLAttributeValue | Invalid or unrecognizable attribute value | XML | ERROR |
BadXMLAttribute | Invalid, unrecognized or malformed attribute | XML | ERROR |
UnrecognizedXMLElement | Element either not recognized or not permitted | XML | ERROR |
BadXMLComment | Badly formed XML comment | XML | ERROR |
BadXMLDeclLocation | XML declaration not permitted in this location | XML | ERROR |
XMLUnexpectedEOF | Reached end of input unexpectedly | XML | ERROR |
BadXMLIDValue | Value is invalid for XML ID, or has already been used | XML | ERROR |
BadXMLIDRef | XML ID value was never declared | XML | ERROR |
UninterpretableXMLContent | Unable to interpret content | XML | ERROR |
BadXMLDocumentStructure | Bad XML document structure | XML | ERROR |
InvalidAfterXMLContent | Encountered invalid content after expected content | XML | ERROR |
XMLExpectedQuotedString | Expected to find a quoted string | XML | ERROR |
XMLEmptyValueNotPermitted | An empty value is not permitted in this context | XML | ERROR |
XMLBadNumber | Invalid or unrecognized number | XML | ERROR |
XMLBadColon | Colon characters are invalid in this context | XML | ERROR |
MissingXMLElements | One or more expected elements are missing | XML | ERROR |
XMLContentEmpty | Main XML content is empty | XML | ERROR |
Enumerator | Meaning |
---|---|
LIBSBML_CAT_INTERNAL | A problem involving the libSBML software itself or the underlying XML parser. This almost certainly indicates a software defect (i.e., bug) in libSBML. Please report instances of this to the libSBML developers. |
LIBSBML_CAT_SYSTEM | A problem reported by the operating system, such as an inability to read or write a file. This indicates something that is not a program error but is outside of the control of libSBML. |
LIBSBML_CAT_XML | A problem in the XML content itself. This usually arises from malformed XML or the use of constructs not permitted in SBML. |
Enumerator | Meaning |
---|---|
LIBSBML_SEV_INFO | The error is actually informational and not necessarily a serious problem. |
LIBSBML_SEV_WARNING | The error object represents a problem that is not serious enough to necessarily stop the problem, but applications should take note of the problem and evaluate what its implications may be. |
LIBSBML_SEV_ERROR | The error object represents a serious error. The application may continue running but it is unlikely to be able to continue processing the same XML file or data stream. |
LIBSBML_SEV_FATAL | A serious error occurred, such as an out-of-memory condition, and the software should terminate immediately. |
Python method signature(s):
getErrorId(XMLError self)long
Returns the identifier of this error.
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inherited |
Python method signature(s):
getErrorIdOffset(XMLError self)long
Returns libSBML's internal numerical offset for the error code associated with this error.
In the SBML Level 3 package specifications, package validation rules are identified by 5-digit numbers prefixed with the nickname of the package itself—e.g., “comp-10101”, “fbc-20301”, etc. Historically, libSBML reported error codes as pure integers, and some application software systems make decisions based on the numerical values of the error codes. To permit these applications to continue to function in this fashion, libSBML internally continues to maintain error identifiers as pure integers. To handle the possibility that errors may come from package extensions, libSBML uses numerical offsets added to the internal error codes. These offsets add two leading digits to the regular 5-digit error codes; for example, “comp” error codes are stored as 1010101, 1020102, etc. The offset in this case is 1000000. Another package will have the offset 2000000, yet another will have 3000000, etc.
This method returns the integer offset in this error's error code. Calling applications can get the 5-digit package-specific number for a given error code by subtracting the offset from the value reported by getErrorId():
getErrorId() - getErrorIdOffset()
When libSBML produces error messages, it combines the text string returned by getPackage() with the subtracted value of the error code, to produce a text string of the form “comp-10101”.
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inherited |
Python method signature(s):
getLine(XMLError self)long
Returns the line number in the XML input near where the error, warning or other diagnostic occurred.
We say 'near where the problem occurred', because many factors affect how accurate the line/column information ultimately is. For example, sometimes, the underlying XML parsers can only report such information for the parent XML element where an error occurs, and not for the specific point where the problem occurs. In other situations, some parsers report invalid line and/or column numbers altogether. If this occurs, libSBML sets the line and/or column number in the XMLError object to either 0
or the value of the maximum unsigned long integer representable on the platform where libSBML is running. The probability that a true line or column number in an SBML model would equal this value is vanishingly small; thus, if an application encounters these values in an XMLError object, it can assume no valid line/column number could be provided by libSBML in that situation.
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inherited |
Python method signature(s):
getMessage(XMLError self)string
Returns the message text of this error.
The message associated with an error object describes the nature of the problem. The message returned by this method is generally longer and clearer than the message returned by XMLError.getShortMessage(), but not in all cases.
Callers may use XMLError.getCategory() and XMLError.getSeverity() to obtain additional information about the nature and severity of the problem.
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inherited |
Python method signature(s):
getPackage(XMLError self)string
Returns the SBML Level 3 package extension (if any) that logged this error.
Each error logged by an libSBML extension for SBML Level 3 packages includes a record of the package that logged it. The field is a simple text string. If the string is empty or has the value 'core'
, then the error came from libSBML core; otherwise, the string will be the short-form name of the package (e.g., 'comp'
for the Hierarchical Model Composition package).
'core'
.
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inherited |
Python method signature(s):
getSeverity(XMLError self)long
Returns the severity of this error.
XMLError defines an enumeration of severity codes for the XML layer. Applications that build on XMLError by subclassing it may add their own severity codes with numbers higher than those in the predefined set of severity codes.
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inherited |
Python method signature(s):
getSeverityAsString(XMLError self)string
Returns a string describing the severity level of this error.
XMLError defines an enumeration of severity codes for the XML layer. Applications that build on XMLError by subclassing it may add their own severity codes with numbers higher than those in the predefined set of severity codes.
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inherited |
Python method signature(s):
getShortMessage(XMLError self)string
Returns a brief message for this error.
This is an alternative error message that, in general, is as short as the authors could make it. However, brevity is often inversely proportional to clarity, so this short message may not be sufficiently informative to understand the nature of the error. Calling applications may wish to check XMLError.getMessage() in addition or instead.
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inherited |
Python method signature(s):
getStandardMessage(int code)string
Returns a copy of the message string associated with the given predefined XMLError code.
code | the error code whose message is sought; it must be a predefined value from the set of predefined error identifiers. |
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inherited |
Python method signature(s):
isError(XMLError self)bool
Predicate returning True
or False
depending on whether this error is a significant error.
This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_ERROR from the set of predefined severity codes.
True
if this error is an error, False
otherwise.
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inherited |
Python method signature(s):
isFatal(XMLError self)bool
Predicate returning True
or False
depending on whether this error is a fatal run-time error.
This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_FATAL from the set of predefined severity codes.
True
if this error is a fatal error, False
otherwise.
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inherited |
Python method signature(s):
isInfo(XMLError self)bool
Predicate returning True
or False
depending on whether this error object is for information purposes only.
This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_INFO from the set of predefined severity codes.
True
if this XMLError is for informational purposes only, False
otherwise.
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inherited |
Python method signature(s):
isInternal(XMLError self)bool
Predicate returning True
or False
depending on whether this error resulted from an internal program error.
This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_INTERNAL from the set of predefined category codes.
True
or False
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inherited |
Python method signature(s):
isSystem(XMLError self)bool
Predicate returning True
or False
depending on whether this error was generated by the operating system.
This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_SYSTEM from the set of predefined category codes.
True
or False
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inherited |
Python method signature(s):
isValid(XMLError self)bool
Predicate returning True
or False
depending on whether this error resulted from a problem or whether it was logged as an unknown error.
This is equivalent to obtaining the error identifier from an XMLError object (via XMLError.getErrorId()) and then comparing it to the value XMLUnknownError or UnknownError from the set of predefined error codes.
True
or False
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inherited |
Python method signature(s):
isWarning(XMLError self)bool
Predicate returning True
or False
depending on whether this error object is a warning.
This is equivalent to obtaining the severity code from an XMLError object (via XMLError.getSeverity()) and then comparing it to the value LIBSBML_SEV_WARNING from the set of predefined severity codes.
True
if this error is a warning, False
otherwise.
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inherited |
Python method signature(s):
isXML(XMLError self)bool
Predicate returning True
or False
depending on whether this error resulted from a problem in the XML input (e.g., an XML syntax error).
This is equivalent to obtaining the category identifier from an XMLError object (via XMLError.getCategory()) and then comparing it to the value LIBSBML_CAT_XML from the set of predefined category codes.
True
or False
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inherited |
Python method signature(s):
setColumn(XMLError self, long column)int
Sets the column number where this error occurred.
column | a long integer, the column number to set. |
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inherited |
Python method signature(s):
setLine(XMLError self, long line)int
Sets the line number where this error occurred.
line | a long integer, the line number to set. |